Friday, May 12, 2017

PRISMs of ISMs


Do Prisms
Create isms
And do
Isms foster
Prisms?

Filtered light
Refracts
Diffuses
Maps
Truism.

Light sheds
It's colors
A blotch
Absorbs
Obscurantism.

The color
Changed
Painted over
With the
Vision
Scientism.

The prism
Floats
One face
Made opaque
Harmed
Idealism.

No light
No refraction
Absolute
Thought
Absolutism.

Multiple lights
Rainbows
Upon
Rainbows
Confusion
Absurdism.

The refraction
Lost
Blocked by
Intention
Anarchism.

The ghost
In Prism
Plays
With our minds
Nihilism.

Refracted colors
On the
Wall
Bright
Luminescent
Racism.

Pixie dust
In prism
From
Mars
Scatters light
Romanticism.

Humans
Profess
Changes
The view
Alters thought
Egoism.

Even Fourier's
Transform
reflects back
to the
bright photon
Originalism.

Although A-posteriori
Of Verified
Concepts
Is Bruno’s
Essentialism

And belief in
Ontological
Nature of
Kuukkanen’s being
Historicism

Both suffer
Godel’s
Incompleteness
Of knowledge
Casualism

Perhaps
Light is light
Splinters
Into colors
As humans
Splinter 
Into isms.

So Prisms
Give rise
To isms
As do isms

To Prisms.


Sunday, April 30, 2017

FRAGILE CONSTRUCTS

On Meaninglessness of Meanings

In isolated silos where the distinguished meet, there follows the wrath of groupthink, emboldened by the weak minds exercising power with even weaker science. Sometime ago one used the Fourier Transform by using multiple filters to dissect an issue of great import and learnt how the mechanics and levers that made the issue tick. That was real. Not anymore. That real science held an importance to humanity and that it would become the shoulders for other giants to climb upon and see further. Time and the proliferation of meaningless degrees in various disciplines force students to see only the trees for the forests. Alas the very idea of real progress has crumbled into mini-false-incrementalism. Today the false prophets of science soar in popularity.



Commoditizing knowledge is a wonderful thing. It leads to fecund minds. But commoditizing nonsense as science is a far, far dangerous thing to do than has been done at such a large scale before. Now possessing a rudimentary knowledge of clicking boxes in a SAS or SPSS program leads one to conjure up meaningless values that define our scientific knowledge-base. We extoll the virtue of binary choice between disparate variables as reality. Correlations they call it are sold in bulk as causality. Compound A “may” help you live longer. The next day the inverse is true as a competing compound takes shape. As John Stuart Mills mentioned the sum of several antecedents are a requisite to produce the consequent (A System of Logic 1843). The fault lies in the choice of the antecedents.



Is science in general and medical science specifically in decline? My real answer is a simple “YES.” As the old advertising goes, “We have come a long way baby,” on the path to self-delusion. There is an added layer of cruelty, greed, self-aggrandizement and recklessness built into this engine of deceit. It is an insult to science, in general and specifically medicine. The whole enterprise is a hijacked engineering marvel of loathsome proportions. Here is where humanity’s claim on life, liberty and the pursuit of happiness is just a phrase for some.



The pursuit of “truth” today is wrapped around Ronald Fisher’s p-value; the sanctified hallmark of significance that medical literature has come to worship, wrongly, I might add. But first let us deconstruct this barbarian indulgence of “Evidence” as it exists today.

On Publishing and Productivity

Let me begin by quoting Peter Higgs, who did pioneering research into fundamental particles back in the 1960s, he groaned “Today I wouldn’t get an academic job. It’s as simple as that. I don’t think I would be regarded as productive enough’ (The Guardian, 6 Dec 2013). 60 years hence that statement rings true even more as real research has been reduced to a plethora of meaningless “studies.”

Today we are mired in a sea of storms. Each storm a concoction from the minds of some very intelligent and some very crafty “scientists.” Both are involved in a race for success. The intellectual may wish it, while the crafty scientist games it. This, as we move forward will become abundantly clear.



First if we look at the explosion in medical literature. From 1974 to 2014, the frequency of the words ‘innovative’, ‘groundbreaking’ and ‘novel’ in PubMed abstracts increased by 2500% or more. (1) The vibrancy of the scientific global industry is evident when more than 15,000,000 people are now authoring more than 25,000,000 scientific papers in a period that scans 15 years (1996–2011). The burgeoning material threatens to remove belief in all things considered science. The pace has only quadrupled in the past 5 years as more “peer-reviewed” journals have appeared that make it impossible for any article to gain any rigor of scrutiny. Journalistic bias to print makes all such studies (true or false, but mostly false) a magnet for Tantalus. (2)

One wonders how this could happen? The answer is simple; “if your career depends on it,” anyone with a shred of intellectual curiosity would answer. Majority of these tenure-seekers have a dim apprehension of the real intellectual currents but a tight grasp on the statistical nuances that exhort their version of reality- and such is the event horizon of our despair. Brischoux and Angelier in 2015 looked at the career stats of junior researchers hired in evolutionary biology between 2005 and 2013. They found persistent increases in the average number of publications at the time of hiring: newly hired biologists now have almost twice as many publications as they did 10 years ago (22 in 2013 versus 12.5 in 2005).” (3)

What is even more curious and abundantly clear is that most new tenure-track positions are filled by graduates from a small number of elite universities—typically those with very high publication rates. This may come as a shock but the truth is easy to see. The more elite your institution, the more likely you get published in a peer-review journal and the more impact you have. You are cited more and that makes the crazy world of scientific merry-go-round reach a dizzying pace, as it feeds on itself.

On Quantifying the Qualitative

In similar vein, using quantitative metrics as a proxy to assess social behavior, opens the concept to exploitation and corruption. Today, quantitative metrics are the hallmark of all qualitative measures and therefore can be exploited to reveal the ether within it in solid form to any sharp-eyed bureaucrat or a "change creator." And that is so much the better for the researcher who gains fame at the cost of exploiting ether. Evidence of this appears in the psychological literature where it is estimated that less than 1% of all psychological research is ever replicated or duplicated! Imagine that for a second. And there is much that goes on in there than meets the eye. The main reason is low-powered studies with small number of case-controlled participants. It reeks of confirmatory bias. The researcher it appears sets out with a premise and proves it with an ideal set of limited variables. Case closed. QED. In other case, hypotheses are being generated at random after the data-sets are at hand, a biased selection of the data easily generates the implied logic of proof, leading to more post hoc hypothesis formation for future publications. (4)



False discoveries in the literature also result from the ongoing fraud of p-hacking (here) http://fivethirtyeight.com/features/science-isnt-broken/
More on that later, but in the same vein, if once considered important studies with high “impact factor” are retracted but their premise has been used to guide other studies, one wonders at the proliferation of the mal content that fills the “evidence” in the scientific libraries. As Retraction Watch states, “The biggest take-home: The number of retracted articles jumped from 500 in Fiscal Year 2014 to 684 in Fiscal Year 2015 — an increase of 37%. But in the same time period, the number of citations indexed for MEDLINE — about 806,000 — has only increased by 5%.” http://retractionwatch.com/2016/03/24/retractions-rise-to-nearly-700-in-fiscal-year-2015-and-psst-this-is-our-3000th-post/



The problem remains the “gaming” nature of this publishing beast. Once set in motion, the authors with an axe to grind, know the “how to” and all credibility is lost. Even those with the best of intentions and stringent ethics get caught up with the statistical serpent. The funding organization may pull strings to get the right results, thus muddying the waters even more. The funders are consigning some if not most newly minted science researchers into the purgatory of fake statistics.



And the wild success of this emptiness inflames the young researcher’s desires and inflates their egos to keep the train of nonsense choo-chooing. Negative results are statistically manipulated to evoke weak signals through “p-hacking” techniques by using selection bias in the carefully codified variables that always yield the desired result. Everyone gets in the game and that, then, becomes the norm. Drawing analogies to the evolutionary quills on the porcupine to protect from predators and guarantee survival are examples of environmental forces similar to what the modern day scientist faces, especially in the publish or perish world.

On Statistics of Simulacra

Cohen states, “Statistical power refers to the probability that a statistical test will correctly reject the null hypothesis when it is false, given information about sample size, effect size and likely rates of false positives.” Science however does not have a mechanism that governs the reliability of the information it imparts. There is no switch or buzzer that rejects the brazen self-interest of the individual scientist to guarantee an optimal result. Science still and always will rely on the integrity of the scientist. Most times the integrity is exposed through the rigors of others that read and desire to understand such results. Vankov et al. suggest that statistical power in psychological science appears to have remained low to the present day (5 and 6). The use of low statistical power is widespread, with no difference between high impact prestigious journals versus their low impact counterparts. (7) What is interesting is even more befuddling that retractions seem to come more often from the “high impact” journals! (8) Never has so much willful blindness meant so little in the advancement of scientific literature. As Macleod et. al. have stated (which should be disconcerting to all who have a stake-hold in the benefits of science) that 85% of the research resources are being wasted in biomedical research. (9) And as the noise begins to reach deafening levels, it becomes difficult to find the signal. “One can decrease the rate of false positives by requiring stronger evidence to posit the existence of an effect. However, doing so will also decrease the power—because even true effects will sometimes generate weak or noisy signals—unless effort is exerted to increase the size and quality of one’s dataset. This follows readily from the logic of signal detection theory.”

On Ionnadis and Ionnadis

Iannodis exposes more contradictions in highly cited clinical research below: “Of 49 highly cited original clinical research studies, 45 claimed that the intervention was effective. Of these, 7 (16%) were contradicted by subsequent studies, 7 others (16%) had found effects that were stronger than those of subsequent studies, 20 (44%) were replicated, and 11 (24%) remained largely unchallenged. Five of 6 highly-cited nonrandomized studies had been contradicted or had found stronger effects vs 9 of 39 randomized controlled trials (P = .008). Among randomized trials, studies with contradicted or stronger effects were smaller (P = .009) than replicated or unchallenged studies although there was no statistically significant difference in their early or overall citation impact. Matched control studies did not have a significantly different share of refuted results than highly cited studies, but they included more studies with "negative" results” (10).
https://www.ncbi.nlm.nih.gov/pubmed/16014596

Ionnadis et. al. write, “we have evaluated by meta-analysis 370 studies addressing 36 genetic associations for various outcomes of disease. We show that significant between-study heterogeneity (diversity) is frequent, and that the results of the first study correlate only modestly with subsequent research on the same association. The first study often suggests a stronger genetic effect than is found by subsequent studies. Both bias and genuine population diversity might explain why early association studies tend to overestimate the disease protection or predisposition conferred by a genetic polymorphism. We conclude that a systematic meta-analytic approach may assist in estimating population-wide effects of genetic risk factors in human disease” (11).

It appears that Le Fanu might have been correct when he professed that all Epidemiology departments should be closed. They should! As Theodore Dalrymple states so eloquently, “for what shall it profit an intellectual if he acknowledges the simple truth and lose his Weltanschauung? Let millions suffer so long as he can retain his sense of his own righteousness and moral superiority.” It is the perverted use of statistical methodology (using the far-reaching claws of correlational fungibles) used in medical research that has caused this rampant misuse/abuse and threatens the very existence and true nature of the value of rigorous medical research/science (12). This ongoing accrual of vast amounts of disinformation is an abysmal bloom of the wanton ignorance pervading the scientific society. The virtue signaling conformity scions are pushing the rest of us into a dark place from where it maybe difficult to return.

On exposing BS

I will leave you with the 2012 AMGEN study that revealed only 6 of 53 (11%) studies in biomedical research were reproducible. Imagine the wishful thinking in the 47 others. The magnitude of this information is staggering. (13) You needn't look further than the latest headlines from Retraction Watch where an estimated 107 papers were retracted from a SINGLE Journal for "Peer Review Fraud!" (also here... http://retractionwatch.com/2017/04/20/new-record-major-publisher-retracting-100-studies-cancer-journal-fake-peer-reviews/ )

REFERENCES:

1.     Vinkers  V, Tijdink  J, Otte  W. 2015 Use of positive and negative words in scientific PubMed abstracts between 1974 and 2014: retrospective analysis. Br. Med. J. 351,
2.     Boyack KW, Klavans R, Sorensen AA, Ioannidis JP (2013) A list of highly influential biomedical researchers, 1996–2011. Eur J Clin Invest 43: 1339–1365.
3.     Brischoux  F, Angelier  F. 2015 Academia’s never-ending selection for productivity. Scientometrics 103, 333–336.
4.     Makel  MC, Plucker  JA, Hegarty  B. 2012 Replications in psychology research: how often do they really occur? Perspect. Psychol. Sci. 7, 537–542.
5.     Cohen  J. 1992 Statistical power analysis. Curr. Dir. Psychol. Sci. 1, 98–101
6.     Vankov  I, Bowers  J, Munafò  MR. 2014 On the persistence of low power in psychological science. Q. J. Exp. Psychol. 67, 1037–1040
7.     Ioannidis  JPA. 2006 Concentration of the most-cited papers in the scientific literature: analysis of journal ecosystems. PLoS ONE 1, e5. (doi:10.1371/journal.pone.0000005)
8.     Fang  FC, Casadevall  A. 2011 Retracted science and the retraction index. Infect. Immun. 79, 3855–3859
9.     Macleod MR, Michie S, Roberts I, Dirnagl U, Chalmers I, et al. (2014) Biomedical research: increasing value, reducing waste. Lancet 383: 101–104.
10.  Ioannidis JPA. Contradicted and initially stronger effects in highly cited clinical research. JAMA. 2005;294:218–22
11.  Ioannidis JPA, Ntzani EE, Trikalinos TA, Contopoulos-Ioannidis DG. Replication validity of genetic association studies. Nat Genet. 2001;29:306–309
12.  Le Fanu J.  The rise and fall of modern medicine. New York: Little, Brown; 1999.

13.  Begley CG, Ellis LM. Drug development: Raise standards for preclinical cancer research. Nature. 2012 Mar 28;483(7391):531-3. doi: 10.1038/483531a.