Category Archives: Philosophical issues raised

You are alive because the lipid bilayer of your plasma membrane is asymmetric

You are an organism with trillions of cells. A mosquito bit you depositing millions of viruses in your tissues. The virus can reproduce only within one of your cells and it has exploited all sorts of protein protein chemistry to get in. Antibodies (if you are fortunate enough to have them) can get rid of the extracellular critters. However, 500,000 have made into the same number of your cells, and are merrily trying to reproduce.

How does the asymmetry of the lipid bilayer of your plasma membrane help you survive. If each virus infected cell killed itself before the virus reproduced, you’d survive. Although 500,000 is a large number is is less than 1 millionth of your cell total.

Well you do have intracellular defenses against viruses, called the innate immune system. One of them is a protein with the ugly name of gasdermin D. The activated innate immune system (in the form of inflammatory caspases) cleaves gasdermin. This breaks up the inhibition of the amino terminal part of gasdermin by the carboxy terminal part giving a fragment which binds to one particular membrane component (phosphatidyl serine) which makes up 20% of the inner leaflet of the cell membrane. It then forms a large diameter (to a cell 140 Angstroms is quite large) pore in the cell membrane. No cell can survive this, so it dies, releasing cellular contents (probably some viral components but not fully formed one). For details see [ Nature vol. 535 pp 111 – 116, 153 – 158 ’16 ]

Wait a minute. The toxic gasdermin fragment is also released. So how come it doesn’t kill everything in sight? Because our cellular membranes keep phosphatidyl serine confined to the inner membrane, normal cells don’t show it on their exterior, so they can be bathed in gasdermin with no ill effect. What is responsible for this asymmetry — believe it or not an ATP consuming enzyme called flippase (about this more later) which takes any phosphatidyl serine it finds on the outer leaflet and schleps it back inside the cell.

There is all sorts of elegant chemistry which explains just how gasdermin binds to phosphatidyl serine and none of the many other phospholipids found on the inner leaflet. There is more elegant chemistry explaining how flippase works (see later).

What chemistry cannot explain, is why organisms would ‘want’ an asymmetric membrane. As soon as you get into the function of a particular compound in an organism, chemistry is powerless to tell you why. Nothing else can explain how a given molecule does what it does on the molecular level but that is not enough for a satisfying explanation.

One further explanation before some hard core cellular biochemistry follows (after ***). Our cells are dying all the time. The lining of your gut is replaced every 5 days. Even the longest lasting element of your blood is gone after half a year, and most other elements are turned over at least once a month. When these cells die, they must be cleaned up, without undue fuss (such as inflammation). The cleaners are cells called macrophages. A dying cell releases chemical signals, actually called ‘eat me’, one of which is phosphatidyl serine found on the membrane fragments of a dead cell. The fact that flippases keep it on the inner leaflet means that macrophages won’t attack a normal cell.

Slick isn’t it?

***

Flippase is a MgATPdependent aminophospholipid translocase. It localizes phosphatidylserine and phosphatidylethanolamine to the inner membrane leaflet by rapidly translocating them from the outer to the inner leaflet against an electrochemical gradient. The stoichiometry between amino phospholipid translocation and ATP hydrolysis is close to one (how will the cell have enough ATP to do anything else?). The flippase is inhibited by high calcium, and by pseudosubstrates such as vanadate, acetylphosphate and para-nitrophenyl phosphate, and by SH reactive reagents such as N-ethylmaleimide and pyridyldithioethylamine (PDA) a specific inhibitor of phospholipid translocation

[ Proc. Natl. Acad. Sci. vol. 109 pp. 1449 – 1454 ’12 ] P4-ATPases are a subfamily of P-type ATPases. They transport aminophospholipids from the exoplasmic to the cytoplasmic leaflet (and are known as flippases). Man has 14 P4-ATPases, expressed in various cell types. They are thought to be similar to the catalytic subunits of the Ca++ ATPase, and the Na, K ATPase, consisting of cytoplasmic, N, P and A domains and a membrane domain made of 10 transmembrane helices (M1 – M10).

[ Proc. Natl. Acad. Sci. vol. 111 pp. E1334 – E1343 ’14 ] The P4-ATPases are thought to resemble the classic P-type ATPase cation pumps — a transmembrane domain of 10 helices and 3 cytoplasmic domains (P for phosphorylation, N for nucleotide binding and A for actuator). ATP8A2 forms an intermediate phosphorylated on aspartic acid (E2P)and undergoes a catalytic cycle similar to the sodium pump (Na+, K+ ATPase). Dephosphorylation of E2P is activated by the transported substrates phosphatidyl serine (PS) and phosphatidyl ethanolamine (PE), similar to the K+ activation of dephosphorylation in the sodium pump.

PE and PS are 10x as large as the cations transported by the sodium pump. This is known as the giant substrate problem. This work shows that isoleucine #364 (mutated in — patients with the ataxia, retardation and dysequilibrium syndrome Eur. J. Hum. Genet. vol. 21 pp. 281 – 285 ’13 aka CAMRQ syndrome ) forms a hydrophobic gate separating the entry and exit sites of PS. I364 likely directs the sequential formation and annihilation of water filled cavities (as shown by molecular dynamics simulations) allowing transport of the hydrophilic phospholipid head group, in a groove outlined by TMs 1, 2, 4 and 6, with the hydrocarbon chains following passively, still in the membrane lipid phase (and presumably outside the channel) — this must disrupt the hell out of the protein as it passes. They call this the credit card model — only the interaction with part of the molecule is important — just as the magnetic stripe is the only important thing about the credit card.

Why you do and don’t need chemistry to understand why we have big brains

You need some serious molecular biological chops to understand why primates such as ourselves have large brains. For this you need organic chemistry. Or do you? Yes and no. Yes to understand how the players are built and how they interact. No because it can be explained without any chemistry at all. In fact, the mechanism is even clearer that way.

It’s an exercise in pure logic. David Hilbert, one of the major mathematicians at the dawn of the 20th century famously said about geometry — “One must be able to say at all times–instead of points, straight lines, and planes–tables, chairs, and beer mugs”. The relationships between the objects of geometry were far more crucial to him than the objects themselves. We’ll take the same tack here.

So instead of the nucleotides Uridine (U), Adenine (A), Guanine (G), Cytosine (C), we’re going to talk about lock and key and hook and eye.

We’re going to talk about long chains of these four items. The order is crucial Two long chains of them can pair up only only if there are segments on each where the locks on one pair with the keys on the other and the hooks with the eyes. How many possible combinations of the four are there on a chain of 20 — just 4^20 or 2^40 = 1,099,511,621,776. So to get two randomly chosen chains to pair up exactly is pretty unlikely, unless in some way you or the blind Watchmaker chose them to do so.

Now you need a Turing machine to take a long string of these 4 items and turn it into a protein. In the case of the crucial Notch protein the string of locks, keys, hooks and eyes contains at least 5,000 of them, and their order is important, just as the order of letters in a word is crucial for its meaning (consider united and untied).

The cell has tons of such Turing machines (called ribosomes) and lots of copies of strings coding for Notch (called Notch mRNAs).

The more Notch protein around in the developing brain, the more the proliferating precursors to neurons proliferate before differentiating into neurons, resulting in a bigger brain.

The Notch string doesn’t all code for protein, at one end is a stretch of locks, keys, hooks and eyes which bind other strings, which when bound cause the Notch string to be degraded, mean less Notch and a smaller brain. The other strings are about 20 long and are called microRNAs.

So to get more Notch and a bigger brain, you need to decrease the number of microRNAs specifically binding to the Notch string. One particular microRNA (called miR-143-3p) has it in for the Notch string. So how did primates get rid of miR-143-3p they have an insert (unique to them) in another string which contains 16 binding sites for miR-143-3p. So this string called lincND essentially acts as a sponge for miR-143-3p meaning it can’t get to the Notch string, meaning that neuronal precursor cells proliferate more, and primate brains get bigger.

So can you forget organic chemistry if you want to understand why we have big brains? In the above sense you can. Your understanding won’t be particularly rich, but it will be at a level where chemical explanation is powerless.

No amount of understanding of polyribonucleotide double helices will tell you why a particular choice out of the 1,099,511,621,776 possible strings of 20 will be important. Literally we have moved from physicality to the realm of pure ideas, crossing the Cartesian dichotomy in the process.

Here’s a copy of the original post with lots of chemistry in it and all the references you need to get the molecular biological chops you’ll need.

Why our brains are large: the elegance of its molecular biology

Primates have much larger brains in proportion to their body size than other mammals. Here’s why. The mechanism is incredibly elegant. Unfortunately, you must put a sizable chunk of recent molecular biology under your belt before you can comprehend it. Anyone can listen to Mozart without knowing how to read or write music. Not so here.

I doubt that anyone can start from ground zero and climb all the way up, but here is all the background you need to comprehend what follows. Start here — https://luysii.wordpress.com/2010/07/07/molecular-biology-survival-guide-for-chemists-i-dna-and-protein-coding-gene-structure/
and follow the links (there are 5 more articles).

Also you should be conversant with competitive endogenous RNA (ceRNA) — here’s a link — https://luysii.wordpress.com/2014/01/20/why-drug-discovery-is-so-hard-reason-24-is-the-3-untranslated-region-of-every-protein-a-cerna/

Also you should understand what microRNAs are — we’re still discovering all the things they do — here’s the background you need — https://luysii.wordpress.com/2015/03/22/why-drug-discovery-is-so-hard-reason-26-were-discovering-new-players-all-the-time/weith.

Still game?

Now we must delve into the embryology of the brain, something few chemists or nonbiological type scientists have dealt with.

You’ve probably heard of the term ‘water on the brain’. This refers to enlargement of the ventricular system, a series of cavities in all our brains. In the fetus, all nearly all our neurons are formed from cells called neuronal precursor cells (NPCs) lining the fetal ventricle. Once formed they migrate to their final positions.

Each NPC has two choices — Choice #1 –divide into two NPCs, or Choice #2 — divide into an NPC and a daughter cell which will divide no further, but which will mature, migrate and become an adult neuron. So to get a big brain make NPCs adopt choice #1.

This is essentially a choice between proliferation and maturation. It doesn’t take many doublings of a NPC to eventually make a lot of neurons. Naturally cancer biologists are very interested in the mechanism of this choice.

Well to make a long story short, there is a protein called NOTCH — vitally important in embryology and in cancer biology which, when present, causes NPCs to make choice #1. So to make a big brain keep Notch around.

Well we know that some microRNAs bind to the mRNA for NOTCH which helps speed its degradation, meaning less NOTCH protein. One such microRNA is called miR-143-3p.

We also know that the brain contains a lncRNA called lncND (ND for Neural Development). The incredible elegance is that there is a primate specific insert in lncND which contains 16 (yes 16) binding sites for miR-143-3p. So lncND acts as a sponge for miR-143-3p meaning it can’t bind to the mRNA for NOTCH, meaning that there is more NOTCH around. Is this elegant or what. Let’s hear it for the Blind Watchmaker, assuming you have the faith to believe in such things.

Fortunately lncND is confined to the brain, otherwise we’d all be dead of cancer.

Should you want to read about this, here’s the reference [ Neuron vol. 90 pp. 1141 – 1143, 1255 – 1262 ’16 ] where there’s a lot more.

Historically, this was one of the criticisms of the Star Wars Missile Defense — the Russians wouldn’t send over a few missles, they’d send hundreds which would act as sponges to our defense. Whether or not attempting to put Star Wars in place led to Russia’s demise is debatable, but a society where it was a crime to own a copying machine, could never compete technically to produce such a thing.

NonAlgorithmic Intelligence

Penrose was right. Human intelligence is nonAlgorithmic. But that doesn’t mean that our physical brains produce consciousness and intelligence using quantum mechanics (although all matter is what it is because of quantum mechanics). The parts (even small ones like neurotubules) contain so much mass that their associated wavefunction is too small to exhibit quantum mechanical effects. Here Penrose got roped in by Kauffman thinking that neurotubules were the carriers of the quantum mechanical indeterminacy. They aren’t, they are just too big. The dimer of alpha and beta tubulin contains 900 amino acids — a mass of around 90,000 Daltons (or 90,000 hydrogen atoms — which are small enough to show quantum mechanical effects).

So why was Penrose right? Because neural nets which are inherently nonAlgorithmic are showing intelligent behavior. AlphaGo which beat the world champion is the most recent example, but others include facial recognition and image classification [ Nature vol. 529 pp. 484 – 489 ’16 ].

Nets are trained on real world images and told whether they are right or wrong. I suppose this is programming of a sort, but it is certainly nonAlgorithmic. As the net learns from experience it adjusts the strength of the connections between its neurons (synapses if you will).

So it should be a simple matter to find out just how AlphaGo did it — just get a list of the neurons it contains, and the number and strengths of the synapses between them. I can’t find out just how many neurons and connections there are, but I do know that thousands of CPUs and graphics processors were used. I doubt that there were 80 billion neurons or a trillion connections between them (which is what our brains are currently thought to have).

Just print out the above list (assuming you have enough paper) and look at it. Will you understand how AlphaGo won? I seriously doubt it. You will understand it less well than looking at a list of the positions and momenta of 80 billion gas molecules will tell you its pressure and temperature. Why? Because in statistical mechanics you assume that the particles making up an ideal gas are featureless, identical and do not interact with each other. This isn’t true for neural nets.

It also isn’t true for the brain. Efforts are underway to find a wiring diagram of a small area of the cerebral cortex. The following will get you started — https://www.quantamagazine.org/20160406-brain-maps-micron-program-iarpa/

Here’s a quote from the article to whet your appetite.

“By the end of the five-year IARPA project, dubbed Machine Intelligence from Cortical Networks (Microns), researchers aim to map a cubic millimeter of cortex. That tiny portion houses about 100,000 neurons, 3 to 15 million neuronal connections, or synapses, and enough neural wiring to span the width of Manhattan, were it all untangled and laid end-to-end.”

I don’t think this will help us understand how the brain works any more than the above list of neurons and connections from AlphaGo. There are even more problems with such a list. Connections (synapses) between neurons come and go (and they increase and decrease in strength as in the neural net). Some connections turn on the receiving neuron, some turn it off. I don’t think there is a good way to tell what a given connection is doing just by looking a a slice of it under the electron microscope. Lastly, some of our most human attributes (emotion) are due not to connections between neurons but due to release of neurotransmitters generally into the brain, not at the very localized synapse, so it won’t show up on a wiring diagram. This is called volume neurotransmission, and the transmitters are serotonin, norepinephrine and dopamine. Not convinced? Among agents modifying volume neurotransmission are cocaine, amphetamine, antidepressants, antipsychotics. Fairly important.

So I don’t think we’ll ever truly understand how the neural net inside our head does what it does.

The higher drivel – II

From the obituary of a leading philosopher at an Ivy League institution. He proposed the following thought experiment to resolve the question of whether objects and relationship exist in the world independently of how we perceive them. This is what bothered Einstein about quantum mechanics, and he is said to have asked Bohr (I think) ” do you think the moon is not there if we don’t look at it”. The thought experiment is a brain placed in a vat by a mad scientist (I’m not making this up). So the brain in the vat — call him Oscar –could not formulate the sentence of “I am a brain in vat” because Oscar has no experience of a real brain or a real vat.

For this they’re currently paying 60K+ a year? It’s the higher drivel.

I read a book by Nozick with similar impossible situations he worried about after a rave review in the New York Times book review a few years ago. It had questions of the order ‘would bubblegum taste the same on the surface of the sun’.

The higher drivel series will appear from time to time — here’s the first one (published 5 years ago)

“The predicament of any tropological analysis of narrative always lies in its own effaced and circuitous recourse to a metaphoric mode of apprehending its object; the rigidity and insistence of its taxonomies and the facility with which it relegates each vagabond utterance to a strict regimen of possible enunciative formations testifies to a constitutive faith that its own interpretive meta-language will approximate or comply with the linguistic form it examines.”

From p. 35 of the NYTimes book review 16 October’11

You could actually major in this stuff (Semiotics) at an Ivy League university (Brown) in the 80’s. According to the article, Semiotics was the third most popular humanities major there at the time.  One son got in in ’86, but (fortunately) didn’t go there.  Nonetheless he was quite interested in Semiotics, hence the name of this blog.  Fortunately the author of the above quote recovered and notes “I now spend more time learning from the insights of science than deconstructing its truth claims.”

What a gigantic waste of time.  Think what Brown could have done by abolishing the department and using the funds for chemistry or mathematics.  The writer tries to salvage something from the experience noting that ‘a striking number of semiotics students have gone on to influential careers in the media and the creative arts.’  Unfortunately this explains a lot about the current media and ‘the creative arts’.

Students were being conned then, and they’re being conned now.  It might not have mattered what you majored in 50+ years ago at an Ivy League university, the world seemed to want us regardless.   A friend majored in Near Eastern studies, was hired by a bank, never saw the MidEast and did quite well.  Not so today.  The waitress serving us last Wednesday at a local bar was a graduate of one of the seven sisters in 2010.  She majored in Sociology and Psychology, is in debt for > 20K for the experience and is unable to find better work.   It isn’t clear what such a major prepares you for other than what she’s doing.  Finding out the distribution of majors of the jobless 20 somethings participating in OWS would be interesting

For a taste of the semiotics world of the 80’s, Google Alan Sokal and read about the fun he had with such a journal — “Social Text”.  Should you  still have the stomach for such things read “The Higher Superstition” by Gross and Levitt, which goes into more detail about Derrida, Foucault and a host of (mostly French) philosophes and what they tried to pull off.

Freud was right, there is an unconscious mind and it’s pretty smart.

Freud has fallen out of favor, with his analogies of the workings of the mind to a steam engine (drives, pressures, releases, displacements), the dominant technology of his day–as the computer is to ours. However, the following paper [ Proc. Natl. Acad. Sci. vol. 113 pp. E616 – E6125 ’16 ] shows that we have an unconscious mind, and that it is mathematically sophisticated (although I don’t think the authors made this point).

[ Proc. Natl. Acad. Sci. vol. 113 pp. E616 – E625 ’16 ] The work used magnetoencephalography (MEG) https://en.wikipedia.org/wiki/Magnetoencephalography, to record brain activity in response to a series of tone pips. MEG is conceptually quite similar to the electrocardiogram (EKG) or the electroencephalogram (EEG), both measuring voltage differences between two electrodes over time. Well, a voltage difference causes an electric current to flow through a conductor, and the nice wet brain is nothing if not that. Anyone who has studied how an electric motor works, knows that an electric current produces a magnetic field, which is what the MEG measures. The great advantage of MEG is that it is temporally precise, and changes can be measured in milliSeconds.

So what did they do? They presented tone pips to an unspecified number of subjects. The relation of one pip to another could either be completely random (RAND) or part of a repeating pattern — say pip pip pip silence silence pip pip pip silence silence (PAT). In one series of experiments, subjects were asked to press a button as soon as the pip sequence went from random to patterned (RAND –> PAT), all this while the MEG was being recorded. In another, they were asked to do this for PAT –> RAND. The subjects were as good as something called the the mathematical ideal observer of the variable order Markov model. It only took one or two random pips after a patterned sequence to notice it and press the button. They could also pick up that a pattern was formed midway through the second repetition of a pattern.

The MEG showed abrupt changes at either transition (RAND –> PAT or PAT –> RAND). The work didn’t stop with just sequences of just one tone. They could use an ‘alphabet of tones’. The subjects could pick up when the number of tones in the alphabet changed, again with MEG values to match.  So they had an independent signal from the MEG show that the brain picked up the transition without requiring any cooperation from the subjects.  All very nice, but anyone who likes music can do this.

Then the subjects were then asked to perform the n-back task, in which the subject is presented with a sequence of stimuli;  and the task consists of indicating when the current stimulus matches the one from n steps earlier in the sequence. Tricky isn’t it? Certainly, something that requires concentration. The load factor n can be adjusted to make the task more or less difficult. You’ve got to hold the sequence just presented in your head so the n-back task is a test of working memory.

Drum roll —

If the tone pips were presented while the subjects were doing the n-back task, the MEG still picked up RAND –> PAT and PAT –> RAND transitions, something the subjects weren’t consciously trying to do.

We know the brain does all sorts of things unconsciously — e.g. breathing. But they are pretty simple. The tests here are conceptually subtle. Your unconscious brain picks up statistical regularities and irregularities without your consciously trying. Who knows what else it does — maybe Freud was right.

Why should this be useful? Well, you’d want to know if a predator is sneaking up on you. The same work should be done with animals performing a task they’ve been trained to do.

SmORFs and DWORFs — has molecular biology lost its mind?

There’s Plenty of Room at The Bottom is a famous talk given by Richard Feynman 56 years ago. He was talking about something not invented until decades later — nanotechnology. He didn’t know that the same advice now applies to molecular biology. The talk itself is well worth reading — here’s the link http://www.zyvex.com/nanotech/feynman.html.

Those not up to speed on molecular biology can find what they need at — https://luysii.wordpress.com/2010/07/07/molecular-biology-survival-guide-for-chemists-i-dna-and-protein-coding-gene-structure/. Just follow the links (there are only 5) in the series.

lncRNA stands for long nonCoding RNA — nonCoding for protein that is. Long is taken to mean over 200 nucleotides. There is considerable debate concerning how many there are — but “most estimates place the number in the tens of thousands” [ Cell vol. 164 p. 69 ’16 ]. Whether they have any cellular function is also under debate. Could they be like the turnings from a lathe, produced by the various RNA polymerases we have (3 actually) simply transcribing the genome compulsively? I doubt this, because transcription takes energy and cells are a lot of things but wasteful isn’t one of them.

Where does Feynmann come in? Because at least one lncRNA codes for a very small protein using a Small Open Reading Frame (SMORF) to do so. The protein in question is called DWORF (for DWorf Open Reading Frame). It contains only 34 amino acids. Its function is definitely not trivial. It binds to something called SERCA, which is a large enzyme in the sarcoplasmic reticulum of muscle which allows muscle to relax after contracting. Muscle contraction occurs when calcium is released from the endoplasmic reticulum of muscle.  SERCA takes the released calcium back into the endoplasmic reticulum allowing muscle to contract. So repetitive muscle contraction depends on the flow and ebb of calcium tides in the cell. Amazingly there are 3 other small proteins which also bind to SERCA modifying its function. Their names are phospholamban (no kidding) sarcolipin and myoregulin — also small proteins of 52, 31 and 46 amino acids.

So here is a lncRNA making an oxymoron of its name by actually coding for a protein. So DWORF is small, but so are its 3 exons, one of which is only 4 amino acids long. Imagine the gigantic spliceosome which has a mass over 1,300,000 Daltons, 10,574 amino acids making up 37 proteins, along with several catalytic RNAs, being that precise and operating on something that small.

So there’s a whole other world down there which we’ve just begun to investigate. It’s probably a vestige of the RNA world from which life is thought to have sprung.

Then there are the small molecules of intermediary metabolism. Undoubtedly some of them are used for control as well as metabolism. I’ll discuss this later, but the Human Metabolome DataBase (HMDB) has 42,000 entries and METLIN, a metabolic database has 240,000 entries.

Then there is competitive endogenous RNA –https://luysii.wordpress.com/2012/01/29/why-drug-discovery-is-so-hard-reason-20-competitive-endogenous-rnas/

Do you need chemistry to understand this? Yes and no. How the molecules do what they do is the province of chemistry. The description of their function doesn’t require chemistry at all. As David Hilbert said about axiomatizing geometry, you don’t need points, straight lines and planes You could use tables, chairs and beer mugs. What is important are the relations between them. Ditto for the chemical entities making us up.

I wouldn’t like that.  It’s neat to picture in my mind our various molecular machines, nuts and bolts doing what they do.  It’s a much richer experience.  Not having the background is being chemical blind..  Not a good thing, but better than nothing.

An uplifting way to start the New Year

This not a scientific post. Going to a memorial service for an old friend hardly seems like an uplifting way to begin the new year. And yet it was. David and I had been friends since ’58 when we were in the same eating club. He also became an M. D. and unfortunately passed away of a slowly dementing illness, probably Alzheimer’s. As a neurologist I could do nothing for him. What little I did accomplish was discussing the scientific aspects with with his wife, explaining the latest breakthroughs she’d read about (which never were). She was a rock, standing by him until the end. Having taken care of many such patients, and having an uncle die of it, I know just how hard this is.

What in the world could be uplifting about something like this? Seeing how David’s intelligence and personality has now marched on through 4 children and (at least) 4 grandchildren. So in a way he really isn’t gone. What was uncanny was seeing David’s eyes staring at me out of his oldest daughter. It really is remarkable, given what we think we know about genetics, and that 10,000 or so of our 20,000 protein coding genes come from one parent, that an offspring will resemble just one parent and not be an amalgam of both. Perhaps just a few genes determine what we look like.

The grandchildren I talked to ranged in age from about 8 to 17. All were smart and articulate. I tried to push them to use their obvious brains to go into research and perhaps prevent or treat what happened to their grandfather. The littlest one said that he was going to be a particle physicist.

I don’t remember talking religion with David or anyone else back in college. There were devout members of the club who would march in glowing after Sunday church, only to be treated by hungover club mates to a chorus of “Onward Christian Soldiers”. One classmate did become the Lutheran Bishop of Western New York, but he certainly didn’t push his religiosity. The most religious one I do remember became a physics professor at Berkeley.

Of course there were remembrances, that of his oldest daughter being the most interesting (to me). She is a religious Christian who clearly loved her father very much, even though he was a professed atheist, although with a strong sense of right and wrong. They used to argue about the existence or nonexistence of God. She and I agreed that he would never do anything that he thought was wrong, probably one of the reasons I liked him (remember the hungover reprobates of a few paragraphs ago). I suppose his daughter now has the last word, but such an argument really has no end.

It was pretty hard to be a doc back in the 60s and 70s watching good people suffer and die, and still conceive of a benevolent creator. “The Plague” by Camus with its hideous death scene of a child pretty much sums up the argument against one.

And yet, now that we know so much more molecular biology, cellular and organismal biochemistry and physiology, our existence seems totally miraculous. I at least have achieved a sense of peace about illness, suffering and death. These things seem natural. What is truly miraculous is that we are well and functional for so long.

You can take or leave the argument from design of Reverend Paley — here it is

“”In crossing a heath, suppose I pitched my foot against a stone, and were asked how the stone came to be there; I might possibly answer, that, for anything I knew to the contrary, it had lain there forever: nor would it perhaps be very easy to show the absurdity of this answer. But suppose I had found a watch upon the ground, and it should be inquired how the watch happened to be in that place; I should hardly think of the answer I had before given, that for anything I knew, the watch might have always been there. … There must have existed, at some time, and at some place or other, an artificer or artificers, who formed [the watch] for the purpose which we find it actually to answer; who comprehended its construction, and designed its use. … Every indication of contrivance, every manifestation of design, which existed in the watch, exists in the works of nature; with the difference, on the side of nature, of being greater or more, and that in a degree which exceeds all computation.”

The more chemistry and biochemistry I know about what’s going on inside us, the harder I find it to accept that this arose by chance.

This does not make me an anti-evoloutionist. One of the best arguments for evolution, is the evidence for descent with modification, one of its major tenets. The fact that we can use one of our proteins to replace one on yeast using our present genetic technology is hard to explain any other way.

Actually to me now, the existence or nonexistence of a creator is irrelevant. The facts of how we are built is not something you need faith about. The awe about it all comes naturally the more we know and the more we find out.

It ain’t the bricks, it’s the plan

Nothing better shows the utility (and the futility) of chemistry in biology than using it to explain the difference between man and chimpanzee. You’ve all heard that our proteins are only 2% different than the chimp, so we are 98% chimpanzee. The facts are correct, the interpretation wrong. We are far more than the protein ‘bricks’ that make us up, and two current papers in Cell [ vol. 163 pp. 24 – 26, 66 – 83 ’15 ] essentially prove this.

This is like saying Monticello and Independence Hall are just the same because they’re both made out of bricks. One could chemically identify Monticello bricks as coming from the Virginia piedmont, and Independence Hall bricks coming from the red clay of New Jersey, but the real difference between the buildings is the plan.

It’s not the proteins, but where and when and how much of them are made. The control for this (plan if you will) lies outside the genes for the proteins themselves, in the rest of the genome (remember only 2% of the genome codes for the amino acids making up our 20,000 or so protein genes). The control elements have as much right to be called genes, as the parts of the genome coding for amino acids. Granted, it’s easier to study genes coding for proteins, because we’ve identified them and know so much about them. It’s like the drunk looking for his keys under the lamppost because that’s where the light is.

We are far more than the protein ‘bricks’ that make us up, and two current papers in Cell [ vol. 163 pp. 24 – 26, 66 – 83 ’15 ] essentially prove this.

All the molecular biology you need to understand what follows is in the following post — https://luysii.wordpress.com/2010/07/07/molecular-biology-survival-guide-for-chemists-i-dna-and-protein-coding-gene-structure/

Briefly an enhancer is a stretch of DNA distinct from the DNA coding for a given protein, to which a variety of other proteins called transcription factors bind. The enhancer DNA and associated transcription factors, then loops over to the protein coding gene and ‘turns it on’ — e.g. causes a huge (megaDalton) enzyme called pol II to make an RNA copy of the gene (called mRNA) which is then translated into protein by another huge megaDalton machine called the ribosome. Complicated no? Well, it’s happening inside you right now.

The faces of chimps and people are quite different (but not so much so that they look frighteningly human). The cell paper studied cells which in embryos go to make up the bones and soft tissues of the face called Cranial Neural Crest Cells (CNCCs). How did they get them? Not from Planned Parenthood, rather they made iPSCs (induced Pluripotent Stem Cells — https://en.wikipedia.org/wiki/Induced_pluripotent_stem_cell) differentiate into CNCCs. Not only that but they studied both human and chimp CNCCs. So you must at least wonder how close to biologic reality this system actually is.

It’s rather technical, but they had several ways of seeing if a given enhancer was active or not. By active I mean engaged in turning on a given protein coding gene so more of that protein is made. For the cognoscenti, these methods included (1) p300 binding (2) chromatin accessibility,(3) H3K4Me1/K3K4me3 ratio, (4) H3K27Ac.

The genome is big — some 3,200,000,000 positions (nucleotides) linearly arranged along our chromosomes. Enhancers range in size from 50 to 1,500 nucleotides, and the study found a mere 14,500 enhancers in the CNCCs. More interestingly 13% of them were activated differentially in man and chimp CNCCs. This is probably why we look different than chimps. So although the proteins are the same, the timing of their synthesis is different.

At long last, molecular biology is beginning to study the plan rather than the bricks.

Chemistry has a great role in this and will continue to do so. For instance, enhancers can be sequenced to see how different enhancer DNA is between man and chimp. The answer is not much (again 2 or so nucleotides per hundred nucleotides of enhancer). The authors did find one new enhancer motif, not seen previously called the coordinator motif. But it was present in man in chimp. Chemistry can and should explain why changing so few nucleotides changes the proteins binding to a given enhancer sequence, and it will be important in designing proteins to take advantage of these changes.

So why is chemistry futile? Because as soon as you ask what an enhancer or a protein is for, you’ve left physicality entirely and entered the realm of ideas. Asking what something is for is an entirely different question than how something actually does what it is for.  The latter question  is answerable by chemistry and physics. The first question is unanswerable by them.  The Cartesian dualism of flesh and spirit is alive and well.

It’s interesting to see how quickly questions in biology lead to teleology.

How ‘simple’ can a protein be and still have a significant biological effect

Words only have meaning in the context of the much larger collection of words we call language. So it is with proteins. Their only ‘meaning’ is the biologic effects they produce in the much larger collection of proteins, lipids, sugars, metabolites, cells and tissues of an organism.

So how ‘simple’ can a protein be and still produce a meaningful effect? As Bill Clinton would say, that depends on what you mean by simple. Well one way a protein can be simple is by only having a few amino acids. Met-enkephalin, an endogenous opiate, contains only 5 amino acids. Now many wouldn’t consider met-enkehalin a protein, calling it a polypeptide instead. But the boundary between polypeptide and protein is as fluid and ill-defined as a few grains of sand and a pile of it.

Another way to define simple, is by having most of the protein made up by just a few of the 20 amino acids. Collagen is a good example. Nearly half of it is glycine and proline (and a modified proline called hydroxyProline), leaving the other 18 amino acids to make up the rest. Collagen is big despite being simple — a single molecule has a mass of 285 kiloDaltons.

This brings us to [ Proc. Natl. Acad. Sci. vol 112 pp. E4717 – E4727 ’15 ] They constructed a protein/polypeptide of 26 amino acids of which 25 are either leucine or isoleucine. The 26th amino acid is methionine (which is found at the very amino terminal end of all proteins — remember methionine is always the initiator codon).

What does it do? It causes tumors. How so? It binds to the transmembrane domain of the beta variant for the receptor for Platelet Derived Growth factor (PDGFRbeta). The receptor when turned on causes cells to proliferate.

What is the smallest known oncoprotein? It is the E5 protein of Bovine PapillomaVirus (BPV), which is an essentially a free standing transmembrane domain (which also binds to PDGFRbeta). It has only 44 amino acids.

Well we have 26 letters + a space. I leave it to you to choose 3 of them, use one of them once, the other two 25 times, with as many spaces as you want and construct a meaningful sequence from them (in any language using the English alphabet).

Just back from an Adult Chamber Music Festival (aka Band Camp for Adults).  More about that in a future post

Is natural selection disprovable?

One of the linchpins of evolutionary theory is that natural selection works by increased reproductive success of the ‘fittest’. Granted that this is Panglossian in its tautology — of course the fittest is what survives, so of course it has greater reproductive success.

So decreased reproductive success couldn’t be the result of natural selection could it? A recent paper http://www.sciencemag.org/content/348/6231/180.full.pdf says that is exactly what has happened, and in humans to boot, not in some obscure slime mold or the like.

The work comes from in vitro fertilization which the paper says is responsible for 2 -3 % of all children born in developed countries — seems high. Maternal genomes can be sequenced and the likelihood of successful conception correlated with a variety of variants. It was found that there is a strong association between change in just one nucleotide (e.g. a single nucleotide polymorphism or SNP) and reproductive success. The deleterious polymorphism (rs2305957) decreases reproductive success. This is based on 15,388 embryos from 2,998 mothers sampled at the day-5 blastocyst stage.

What is remarkable is that the polymorphism isn’t present in Neanderthals (from which modern humans diverged between 100,000 and 400,000 year ago). It is in an area of the genome which has the characteristics of a ‘selective sweep’. Here’s the skinny

A selective sweep is the reduction or elimination of variation among the nucleotides in neighbouring DNA of a mutation as the result of recent and strong positive natural selection.

A selective sweep can occur when a new mutation occurs that increases the fitness of the carrier relative to other members of the population. Natural selection will favour individuals that have a higher fitness and with time the newly mutated variant (allele) will increase in frequency relative to other alleles. As its prevalence increases, neutral and nearly neutral genetic variation linked to the new mutation will also become more prevalent. This phenomenon is called genetic hitchhiking. A strong selective sweep results in a region of the genome where the positively selected haplotype (the mutated allele and its neighbours) is essentially the only one that exists in the population, resulting in a large reduction of the total genetic variation in that chromosome region.

So here we have something that needs some serious explaining — something decreasing fecundity which is somehow ‘fitter’ (by the definition of fitness) because it spread in the human population. The authors gamely do their Panglossian best explaining “the mitotic-error phenotype (which causes decreased fecundity) may be maintained by conferring both a deleterious effect on maternal fecundity and a possible beneficial effect of obscured paternity via a reduction in the probability of successful pregnancy per intercourse. This hypothesis is based on the fact that humans possess a suite of traits (such as concealed ovulation and constant receptivity) that obscure paternity and may have evolved to increase paternal investment in offspring.

Nice try fellas, but this sort of thing is a body blow to the idea of natural selection as increased reproductive success.

There is a way out however, it is possible that what is being selected for is something controlled near to rs2305957 so useful, that it spread in our genome DESPITE decreased fecundity.

Don’t get me wrong, I’m not a creationist. The previous post https://luysii.wordpress.com/2015/04/07/one-reason-our-brain-is-3-times-that-of-a-chimpanzee/ described some of the best evidence we have in man for another pillar of evolutionary theory — descent with modification. Here duplication of a single gene since humans diverged from chimps causes a massive expansion of the gray matter of the brain (cerebral cortex).

Fascinating

Addendum 13 April

I thought the following comment was so interesting that it belongs in the main body of the text

Handles:

Mutations dont need to confer fitness in order to spread through the population. These days natural selection is considered a fairly minor part of evolution. Most changes become fixed as the result of random drift, and fitness is usually irrelevant. “Nearly neutral theory” explains how deleterious mutations can spread through a population, even without piggybacking on a beneficial mutation; no need for panglossian adaptive hypotheses.

Here’s my reply

Well, the authors of the paper didn’t take this line, but came up with a rather contorted argument to show why decreased fecundity might be a selective advantage, rather than just saying it was random drift. They also note genomic evidence for a ‘selective sweep’ — decreased genomic heterogeneity around the SNP.

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