Hillary’s stroke

Hillary Clinton had a stroke toward the end of 2012. It was not due to the faint she had presumably because of the flu in mid December. The information given out at the time was extremely sketchy and confusing (see the copy of the post of 31 Dec ’12 at the end).

She fainted while giving a speech in Buffalo according to one account and at her home in Washington according to another and was not hospitalized. She is said to have suffered a concussion when she fell. Then on the 30th of December she was hospitalized because a blood clot was found (more later) and placed on blood thinners. She suffered double vision and had to wear corrective glasses (Fresnel lenses) for congressional testimony 23 January 2013.

So she had a blood clot in her head and a neurologic deficit persisting for a few weeks. That’s what a stroke is.

Could it have been due to the head trauma? This is extremely doubtful based on an intense 42 month experience managing acute head injuries.

To get my kids through college, I took a job working for two busy neurosurgeons. When I got there, I was informed that I’d be on call every other night and weekend, taking first call with one of the neurosurgeons backing me up. Neurologists rarely deal with acute head trauma although when the smoke clears we see plenty of its long term side effects (post-traumatic epilepsy, cognitive and coordination problems etc. etc.). I saw plenty of it in soldiers when I was in the service ’68 – ’70, but this was after they’d been stabilized and shipped stateside. Fortunately, my neurosurgical backup was excellent, and I learned and now know far more about acute head trauma than any neurologist should.

We admitted some of the head trauma cases to our service, but most cases had trauma to other parts of the body, so a general surgeon would run the show with our group as consultants. The initial consultant in half the cases was me. If I saw them initially, I followed the patients until discharge. On weekends I covered all our patients and all our consults, usually well over 20 people.

We are told that Hillary had a clot in one of the large draining veins in the back of her head (venous sinuses actually). In all the head trauma I saw (well over 300 I’d guess), I never saw a clot develop there. I’ve spoken to two neuroradiologists still in practice, and they can’t recall seeing such a clot without a skull fracture near the vein. Nothing like this was mentioned at any time about Hillary.

Hillary’s neurologic deficit involved a nerve going to the muscles of her left eye. These start in the brainstem, a part of the brain quite near the site where she is said to have the clot in her vein. The brainstem is crucial in maintaining consciousness, and it is far more likely that the faint in early December was a warning sign of the stroke she had subsequently.

I can’t believe that she would not have been hospitalized had she complained of double vision when she fainted in early December, so it must have come on later.

So the issue is why did she have the stroke, and how likely is it to recur. I seriously doubt that it had anything to do with the head injury she sustained when she fainted. We’ve have two presidents neurologically impaired by stroke in the past century (Woodrow Wilson after World War I and Franklin Delano Roosevelt at Yalta). The results were not happy for the USA or the World.

Certainly all this would be cleared up if her medical records were released. Only Hillary can do this, but at least she cannot destroy them, as although she ‘owns’ them, they are not in her sole possession.

The following is a post written 31 December ’12 when the news of Hillary’s illness first broke showing how fragmentary the information about it was back then (it isn’t a good deal better now).

Medical tribulations of politicians — degrees of transparency

Remarkably on the last day of the year, 3 political figures and their medical problems are in the news. Here they are in order of medical transparency (highest first).

l. George Bush Sr. — the most transparent. We are told what he has (pneumonia), when he was admitted to hospital when he was in the ICU, when he came out. Docs call pneumonia ‘the old man’s friend’ not out of cynicism, but because its a mode of death with (relatively) little suffering. The patient lapses into unconsciousness and usually dies quickly and quietly. It took my cellist’s father only a day or two to pass away this month. Clearly it isn’t invariably fatal, and Bush Sr. was now out of the ICU at last count (he’s 88).

2. Hillary Clinton — admitted to the hospital yesterday with a ‘blood clot’ somewhere, said to be a complication of the concussion she suffered a few weeks ago. Also said to be under treatment with anticoagulants. Most clots due to head trauma are inside the head and treating them with anticoagulants is a disaster. The most likely type of clot given the time from the concussion is a subdural hematoma. It is possible that she’s been so inactive since the concussion that she developed thrombophlebitis in her legs, in which case anticoagulation would be indicated.

More disturbingly, is that her passing out a few weeks ago is a sign of something more serious going on. Hopefully not.

The powers that be should have told us where the clot actually is.

Update 5:50 PM EST — Well the powers that be did open up and it is a most unusual complication of head injury (and one I’d never seen in nearly 4 decades of practice) — a venous thrombosis in the head. I’m not even sure it’s due to her head injury. It might have even caused her syncope, but presumably she had some sort of radiologic study of her head when she fainted, which should have picked it up. The venous sinuses draining the brain in the back of the head are notoriously asymmetric, so a narrowing attributable to a clot could just be a variant anatomy. One very bad complication of cerebral venous thrombosis back there (which I saw as a complication of chronic mastoid bone infection — not head trauma) is pseudotumor cerebri. I really wonder if these guys have the right diagnosis.

3. Hugo Chavez — Yesterday it was announced that he’s had a third complication since his surgery for cancer 3 weeks ago. Naturally, we’re not told just what this complication actually is. This is consistent with the information that has been released about his case. We know almost nothing about his actual tumor (except that he has one). He most assuredly is not free of cancer as he stated last fall. He is said to have have a bleeding problem and a lung infection as the first two complications.

My guess for this third complication is that it is a dehiscence of his abdominal incision, which must have been fairly large for a 6 hour operation. Dehiscence just means that the wound has spontaneously opened up exposing abdominal contents (which means that peritonitis is not far behind). Why should this happen? Two reasons — he’s had radiation to the area which inhibits wound healing, and he’s been on high dose steroids in the past (and perhaps presently) which also inhibits wound healing.

I don’t think he’s going to be able to take office 10 days hence, and doubt that he’ll come back to Venezuela alive. Transparency has been zilch. Hopefully the people of Venezuela are beginning to realize just how misleading the information they’ve been fed about his health has been.

This is the sort of thing physicians taking care of really sick people deal with daily, which may explain why your doc friends aren’t as jolly as you are at the New Year’s Eve parties you’re about to attend.

Nonetheless, Happy New Year to all ! ! ! !

None dare call it junk

There has been a huge amount of controversy about whether all the DNA we carry about has some purpose to carry out — or not. Could some of it be ‘junk’?.

At most 2% of our DNA actually codes for the amino acids comprising our proteins. Some (particularly the ENCODE consortium) have used the criterion of transcription of the DNA into RNA (a process which takes energy) as a sign that well over 50% of our genome is NOT junk. Others regard this transcription as the unused turnings from a lathe.

All agree however, that bacteria use a good deal of their small genomes to code for protein. The following paper http://www.pnas.org/content/112/14/4251.full quotes a figure of 84 – 89%.

Consider the humble leprosy organism.It’s a mycobacterium (like the organism causing TB), but because it essentially is confined to man, and lives inside humans for most of its existence, it has jettisoned large parts of its genome, first by throwing about 1/3 of it out (the genome is 1/3 smaller than TB from which it is thought to have diverged 66 million years ago), and second by mutation of many of its genes so protein can no longer be made from them. Why throw out all that DNA? The short answer is that it is metabolically expensive to produce and maintain DNA that you’re not using

If you want a few numbers here they are:
Genome of M. TB 4,441,529 nucleotides
Genome of M. Leprae 3,268,203 nucleotides
1,604 genes coding for protein
1,116 pseudoGenes (e.g. genes that look like they could code for proteins, but no longer can because of premature termination codons.

This brings us to the organism described in the paper — Trichodesmium erythraeum — a photosynthetic bacterium living in the ocean. When conditions are right it multiplies rapidly causing a red algal bloom (even though it isn’t an algae which are cellular). It’s probably how the Red Sea got its name.

The organism only uses 64% of its genome to code for its protein. The most interesting point is that 86% of the nonCoding (for protein anyway) DNA is transcribed into RNA.

The authors wrestle with the question of what the nonCoding DNA is doing.

“Because it is thought that many bacteria are deletion-biased (47, 77), stable maintenance of these elements from laboratory isolates to the natural samples suggest that they may be required in some fashion for growth both in culture and in situ.”

Translation: The nonCoding DNA probably isn’t junk.

They give it another shot.

“Others have hypothesized that the conserved repeat structures observed in some bacteria could function as recombination-dependent “promoter banks” for adaptation to new conditions, thereby allowing relatively quick “rewiring” of metabolism in subpopulations”

Plausible, but why waste the energy transcribing the DNA into RNA if it isn’t doing anything for the organism doing the transcribing?

Never assume that what you can’t measure or don’t understand is unimportant.

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.

One reason our brain is 3 times that of a chimpanzee

Just based on the capacity of the skull, our brain is 3 – 4 times larger than that of our closest primate relative, the chimp. Most of the increase in size occurs in the cerebral cortex (the gray matter) just under the skull. Our cortex is thrown into folds because there is so much of it. Compare the picture of the mouse brain (smooth) and ours, wrinkled like a walnut http://www.nsf.gov/discoveries/disc_summ.jsp?cntn_id=130442.

We now may have part of the explanation. A fascinating paper http://www.sciencemag.org/content/347/6229/1465.full.pdf studied genetic differences between the progenitor cells from which the cortex arises (radial glia) in man and mouse. They found 56 protein coding genes expressed in our radial glia not present in the mouse (out of 20,000 or so).

One in particular called by the awful name ARHGAP11B is particularly fascinating. Why? Because it’s the product of a gene duplication of ARHGAP11A. When did this happen — after the human line split off from the chimp 6 million years ago. Chimps have no such duplication, just the original

Put ARHGAP11B into a developing mouse and its cortex expands so much it forms folds.

There has been all sorts of work on the genetic difference between man and chimp. There almost too many — [ Nature vol. 486 pp. 481 – 482 ’12 ] — some 20,000,000. Finding the relevant ones is the problem. ARHGAP11A is by far the best we’ve found to date.

Another fascinating story is the ‘language gene’ discovered in a family suffering from a speech and language disorder. It’s called FOXP2. Since the last common ancestor of humans and mice (70 megaYears ago) there have been only 3 changes in the 715 amino acids comprising the protein. 2 of them have occurred in the human lineage since it split with the chips 6 megaYears ago. So far no one has put the human FOXP2 gene into a chimp and got it to talk. For more details see http://en.wikipedia.org/wiki/FOXP2

There is all sorts of fascinating molecular biology about what these two genes actually do in the cell, but that would make this post too long,. This is, in part, a chemistry blog and just what FOXP2 and ARHGAP11A actually do involves some beautiful and elegant chemistry — look up RhoGAP and Winged Helix transcription factors. Ferrari’s are beautiful cars, and become even more beautiful when you understand what’s going on under the hood. Chemistry gives you that for molecular, cellular and organismal biology.

Of what use is an inactive enzyme?

Why should a cell take the trouble make an enzyme protein with no enzymatic activity? It takes metabolic energy to store the information for a protein in DNA, transcribe the DNA into RNA and then translate the RNA into protein. Is this junk protein a la junk DNA? Not at all — and therein lies a tale.

All sorts of nasty bugs inveigle their way into cells, among them viruses (such as influenza) whose genome is made of RNA, rather than DNA. Not only that, but in many virus their genome is not single stranded (like mRNA) but double stranded with two RNA strands base paired to each other (just like DNA, except for an extra oxygen on the ribose sugars in the backbone).

Nucleated cells don’t contain much double stranded RNA (dsRNA) outside the nucleus, so it almost always means trouble. An extremely elegant mechanism exists to find and respond to such RNA. Recall that double helix molecules can reach enormous lengths.The 3.2 billion base pairs of our genome, if stretched out, would be more than a yard.

Well we have at least 4 genes which bind dsRNA and then signal trouble. They all make a molecule called 2′ – 5′ oligoadenyic acid (2-5A) from ATP, so they are called OligoAdenylate Syntheses (OASs). The 2-5A, once made wanders about the cell until it finds another enzyme called RNAase L. 2-5A binds to RNAase L causing it to dimerize and become active. RNAase L then destroys all the RNA in the cell, killing it along with the invading virus. Pretty harsh, but it’s one way to stop the virus from spreading and killing more cells.

A recent paper http://www.pnas.org/content/112/13/3949.full concerns OAS3, which has 3 catalytic modules rather than just one like most enzymes. Even worse, 2 of the 3 catalytic modules can’t make 2-5A (but they still can bind dsRNA). OAS3 is a large protein (over 1,000 amino acids), so it has some length to it. The 3 catalytic modules are spread out along OAS3 with the active catalytic module at one end and one of the inactive modules at the other.

The modules at both ends bind dsRNA, but only the active module makes 2-5A when it does. Interestingly, the inactive module binds dsRNA much more strongly than the active one.

OK, you’ve got the picture — what possible use is this rather Byzantine set up?

See if you can figure it out.

It’s incredibly clever and elegant, and shows the danger to regarding anything within the cell as functionless (or junk). Teleology rides supreme in molecular and cellular biology.

Give up?

OAS3 essentially acts as a molecular ruler making 2-5A only when long dsRNA (e.g. over 50 nucleotides long) binds to it. The inactive module gloms onto longish dsRNA, holding it tightly until till Brownian motion brings it to the other end of OAS3 activating the catalytic module to make 2-5A. This is good as the cell normally contains all sorts of shorter RNA duplexes (the binding of microRNAs to the 3′ end of mRNAs come to mind — but they are much shorter (22 nucleotides at most).

No wonder we get sick

“It is estimated that a human cell repairs 10,000 – 20,000 DNA lesions per day” This is the opening sentence of Proc. Natl. Acad. Sci. vol. 112 pp. 3997 – 4002 ’15, but no source for this estimate is given. The lesions range from single and double strand breaks in the sugar phosphate backbone of the DNA helix, to hydrolytic losses of a DNA base from the backbone, to chemical modification of the DNA bases themselves — oxidation etc. etc.

What needs explaining then, is why we stay as well as we do. https://luysii.wordpress.com/2009/09/17/the-solace-of-molecular-biology/

Why we imperfectly understand randomness the way we do.

The cognoscenti think the average individual is pretty dumb when it comes to probability and randomness. Not so, says a fascinating recent paper [ Proc. Natl. Acad. Sci. vol. 112 pp. 3788 – 3792 ’15 ] http://www.pnas.org/content/112/12/3788.abstract. The average joe (this may mean you) when asked to draw a random series of fifty or so heads and tails never puts in enough runs of heads or runs of tails. This leads to the gambler’s fallacy, that if an honest coin gives a run of say 5 heads, the next result is more likely to be tails.

There is a surprising amount of structure lurking within purely random sequences such as the toss of a fair coin where the probability of heads is exactly 50%. Even with a series with 50% heads, the waiting time for two heads (HH) or two tails (TT) to appear is significantly longer than for an alternation (HT or TH). On average 6 tosses will be required for HH or TT to appear while only an average of 4 are needed for HT or TH.

This is why Joe SixPack never puts in enough runs of Hs or Ts.

Why should the wait be longer for HH or TT even when 50% of the time you get a H or T. The mean time for HH and TT is the same as for HT and TH. The variance is different because the occurrences of HH and TT are bunched in time, while the HT and TH are spread evenly.

It gets worse for longer repetitions — they can build on each other. HHH contains two instances of HH, while alterations do not. Repetitions bunch together as noted earlier. We are very good at perceiving waiting times, and this is probably why we think repetitions are less likely and soon to break up.

The paper goes a lot farther constructing a neural model, based on the way our brains integrate information over time when processing sequences of events. It takes into consideration our perceptions of mean time AND waiting times. We average the two. This produces the best fitting bias gain parameter for an existing Bayesian model of randomness.

See, you’re not as dumb as they thought you were.

Another reason for our behavior comes from neuropsychology and physiological psychology. We have ways to watch the electrical activity of your brain and find out when you perceive something as different. It’s called mismatch negativity (see http://en.wikipedia.org/wiki/Mismatch_negativity for more detail). It a brain potential (called P300) peaking .1 -.25 seconds after a deviant tone or syllable.

Play 5 middle c’s in a row followed by a d than c’s again. The potential doesn’t occur after any of the c’s just after the d. This has been applied to the study of infant perception long before they can speak.

It has shown us that asian and western newborn infants both hear ‘r’ and ‘l’ quite well (showing mismatch negativity to a sudden ‘r’ or ‘l’ in a sequence of other sounds). If the asian infant never hears people speaking words with r and l in them for 6 months, it loses mismatch negativity to them (and clinical perception of them). So our brains are literally ‘tuned’ to understand the language we hear.

So we are more likely to notice the T after a run of H’s, or an H after a run of T’s. We are also likely to notice just how long it has been since it last occurred.

This is part of a more general phenomenon — the ability of our brains to pick up and focus on changes in stimuli. Exactly the same phenomenon explains why we see edges of objects so well — at least here we have a solid physiologic explanation — surround inhibition (for details see — http://en.wikipedia.org/wiki/Lateral_inhibition). It happens in the complicated circuitry of the retina, before the brain is involved.

Philosophers should note that this destroys the concept of the pure (e.g. uninterpreted) sensory percept — information is being processed within our eyes before it ever gets to the brain.

Update 31 Mar — I wrote the following to the lead author

” Dr. Sun:

Fascinating paper. I greatly enjoyed it.

You might be interested in a post from my blog (particularly the last few paragraphs). I didn’t read your paper carefully enough to see if you mention mismatch negativity, P300 and surround inhibition. if not, you should find this quite interesting.

Luysii

And received the following back in an hour or two

“Hi, Luysii- Thanks for your interest in our paper. I read your post, and find it very interesting, and your interpretation of our findings is very accurate. I completely agree with you making connections to the phenomenon of change detection and surround inhibition. We did not spell it out in the paper, but in the supplementary material, you may find some relevant references. For example, the inhibitory competition between HH and HT detectors is a key factor for the unsupervised pattern association we found in the neural model.

Yanlong”

Nice ! ! !

Should pregnant women smoke pot?

Well, maybe this is why college board scores have declined so much in recent decades that they’ve been normed upwards. Given sequential MRI studies on brain changes throughout adolescence (with more to come), we know that it is a time of synapse elimination. (this will be the subject of another post). We also know that endocannabinoids, the stuff in the brain that marihuana is mimicking, are retrograde messengers there, setting synaptic tone for information transmission between neurons.

But there’s something far scarier in a paper that just came out [ Proc. Natl. Acad. Sci. vol. 112 pp. 3415 – 3420 ’15 ]. Hedgehog is a protein so named because its absence in fruitflies (Drosophila) causes excessive bristles to form, making them look like hedgehogs. This gives you a clue that Hedgehog signaling is crucial in embryonic development. A huge amount is known about it with more being discovered all the time — for far more details than I can provide see http://en.wikipedia.org/wiki/Hedgehog_signaling_pathway.

Unsurprisingly, embryonic development of the brain involves hedgehog, e,g, [ Neuron vol. 39 pp. 937 – 950 ’03 ] Hedgehog (Shh) signaling is essential for the establishment of the ventral pattern along the whole neuraxis (including the telencephalon). It plays a mitogenic role in the expansion of granule cell precursors during CNS development. This work shows that absence of Shh decreases the number of neural progenitors in the postnatal subventricular zone and hippocampus. Similarly conditional inactivation of smoothened results in the formation of fewer neurospheres from progenitors in the subventricular zone. Stimulation of the hedgehog pathway in the mature brain results in elevated proliferation in telencephalic progenitors. It’s a lot of unfamiliar jargon, but you get the idea.

Of interest is the fact that the protein is extensively covalently modified by lipids (cholesterol at the carboxy terminal end and palmitic acid at the amino terminal end. These allow hedgehog to bind to its receptor (smoothened). It stands to reason that other lipids might block this interaction. The PNAS work shows this is exactly the case (in Drosophila at least). One or more lipids present in Drosophila lipoprotein particles are needed in vivo to keep Hedgehog signaling turned off in wing discs (when hedgehog ligand isn’t around). The lipids destabilize Smoothtened. This work identifies endocannabinoids as the inhibitory lipids from extracts of human very low density lipoprotein (VLDL).

It certainly is a valid reason for women not to smoke pot while pregnant. The other problem with the endocannabinoids and exocannabinoids (e.g. delta 9 tetrahydrocannabinol), is that they are so lipid soluble they stick around for a long time — see https://luysii.wordpress.com/2014/05/13/why-marihuana-scares-me/

It is amusing to see regulatory agencies wrestling with ‘medical marihuana’ when it never would have gotten through the FDA given the few solid studies we have in man.

A post which may actually be of some use to Safari users

This post may actually be of some use (to those of you using Safari on a Mac anyway). Yesterday, I had the awful experience of a pop-up that I couldn’t get rid of. It said that I had to call a number right away to protect my identity etc. etc. I’d heard about malware that got on your computer encrypting everything so you couldn’t use it, except to pay them a ransom.

So I tried quitting Safari and restarting. No luck. There it was along with sites I always go to on Safari (PNAS, Nature, Science, Cell and Neuron).

So I tried to shut down (which wasn’t possible because I got a note that Safari was busy).

Then I used Force Quit to shut down Safari and was then able to shut down.

Rebooting was of no help whatsoever, as the pop-up appeared along with all 5 sites I usually have open whenever I opened Safari. This happened several times, yours truly being bull headed enough to try it again and again against all hope.

Time to call Applecare — they fixed it immediately. Apparently Safari has a some sore of cache which reopens everything you’ve opened on your last visit. This is what brought up my favored sites and the annoying popup.

The trick is to Open Safari from the Dock (and you must do it this way, not from recently used items) with the shift key held down — this flushed the cache (and the pop-up along with it).

Applecare said this pop-up wasn’t malware, just a scam which charged money to get rid of it (which you can now do free of charge).

Why drug discovery is so hard: Reason #26 — We’re discovering new players all the time

Drug discovery is so very hard because we don’t understand the way cells and organisms work very well. We know some of the actors — DNA, proteins, lipids, enzymes but new ones are being discovered all the time (even among categories known for decades such as microRNAs).

Briefly microRNAs bind to messenger RNAs usually decreasing their stability so less protein is made from them (translated) by the ribosome. It’s more complicated than that (see later), but that’s not bad for a first pass.

Presently some 2,800 human microRNAs have been annotated. Many of them are promiscuous binding more than one type of mRNA. However the following paper more than doubled their number, finding some 3,707 new ones [ Proc. Natl. Acad. Sci. vol. 112 pp. E1106 – E1115 ’15 ]. How did they do it?

Simplicity itself. They just looked at samples of ‘short’ RNA sequences from 13 different tissue types. MicroRNAs are all under 30 nucleotides long (although their precursors are not). The reason that so few microRNAs have been found in the past 20 years is that cross-species conservation has been used as a criterion to discover them. The authors abandoned the criterion. How did they know that this stuff just wasn’t transcriptional chaff? Two enzymes (DROSHA, DICER) are involved in microRNA formation from larger precursors, and inhibiting them decreased the abundance of the ‘new’ RNAs, implying that they’d been processed by the enzymes rather than just being runoff from the transcriptional machinery. Further evidence is that of half were found associated with a protein called Argonaute which applies the microRNA to the mRBNA. 92% of the microRNAs were found in 10 or more samples. An incredible 23 billion sequenced reads were performed to find them.

If that isn’t complex enough for you, consider that we now know that microRNAs bind mRNAs everywhere, not just in the 3′ untranslated region (3′ UTR) — introns, exons. MicroRNAs also bind pseudogenes, SINEes, circular RNAs, nonCoding RNAs. So it’s a giant salad bowl of various RNAs binding each other affecting their stability and other functions. This may be echoes of prehistoric life before DNA arrived on the scene.

It’s early times, and the authors estimate that we have some 25,000 microRNAs in our genome — more than the number of protein genes.

As always, the Category “Molecular Biology Survival Guide” found on the left should fill in any gaps you may have.

One rather frightening thought; If, as Dawkins said, we are just large organisms designed to allow DNA to reproduce itself, is all our DNA, proteins, lipids etc, just a large chemical apparatus to allow our RNA to reproduce itself? Perhaps the primitive RNA world from which we are all supposed to have arisen, never left.

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