Tuesday, October 21, 2014

Take the Money and Run!

Economists are a strange breed and European ones are the most strange. In a recent Think Progress posting they discuss a paper written by a German post-doc and a German Prof at U Penn. The article states:

A 90 percent tax rate on the top 1 percent of American earners wouldn’t just significantly reduce income and wealth inequality and boost government tax revenues. It would also be the optimal level for Americans’ welfare, according to a new paper from economists ... They find that the top marginal tax rate that maximizes government revenues before being so high as to discourage the wealthiest from earning more is very high, or 95 percent on those who are among the top 1 percent of earners. They also find that a 90 percent tax rate on the richest 1 percent could significantly reduce the Gini index, a measure of income inequality, and wealth inequality would also steadily decline. 

Now being in the top 1% does not mean a great deal if one lives in New York City or in almost all of California. In New York City one's marginal tax rate is 39% Federal, plus 14% City and State, plus 3.5% Medicare. That is 56.5% out the gate, well on the way to the above proposed target.

But the real question one should ask is who best redistributes money. Often those in the top 1% are major donors to Universities and Medical Centers as well as the Arts. For example one need only look at the Hospitals on First Avenue above 61st Street and see what the donors have done. Then compare that to a VA Hospital. It shows that the top 1% create much better outcomes in their redistribution. They really pay attention to what happens with what they give. Unlike the Federal Government whose "gifts" honor former politicians and enrich donors to campaigns. A second example is the New York Botanical Garden, supported by the top 1% and open to all who can come in and explore nature in a pristine location within the confines of New York City.

The question then simply is: who is the best re-distributor of others hard earned wealth, a collection of individuals or the Government. The answer is obvious, especially after examining the Government in the past six years. Individuals make better decisions than any Government official.

Furthermore it seems clear that some German economist most likely will never truly understand the way individualism would and has worked to make the United States what it is today. In my experience they have already two strikes against them; first they are economists and second they are Germans. As economists they see the world through often false paradigms, and from that they develop mathematical models to justify their views. Second, as Germans, based upon my decades of experience, they come from a culture of collectivism and with no inkling of individualism. As individualism was a discovery for de Tocqueville, at least he saw it in action, there never has been such a German equivalent.

Thus what we see coming from these economists in my opinion is their world view, which is reflective more of them than any reality that may exist in Nature.

Monday, October 20, 2014

Ebola and Politics

Ebola has been around for decades, and most likely longer albeit hidden in small communities in Central Africa. The current outbreak is most likely due to a failure of local Health Care systems to manages its spread. What makes Ebola and its sister viruses so worrisome if the way they cause mortality, they just decompose the body's cells at surfaces so that there is bleeding from every possible location in the victim. It is nasty, and highly contagious in the right circumstances. Nigeria seems to have controlled it, the other three countries seem to have let it run loose, most likely due to lack of infrastructure and leadership.

Now to the US. Clearly Texas has been a clear case of "dumb and dumber". All those who touched this issue demonstrated their ineptness and lack of preparedness. Yet it seems that certain commentators want to make this even more political. Take for example the Left wing blog, Syndicate, whose commentator states:

But, as recent events have illustrated, robust health agencies should not be taken for granted. In fact, over the past decade, the government has slashed budgets at several top health agencies, including the CDC, the National Institutes of Health (NIH), and state and local health departments. Between 2005 and 2012, for example, the CDC lost 17% of its funding, and officials recently reported that funding allocated for Ebola-type health emergencies is $1 billion less than it was in 2003.
 Now if we go back a century to the early 20th we see such massive outbreaks of TB and Influenza, much less of a budget but highly competent Public Health people. I recall my grandmother's tales of Seaview Hospital on Staten Island, the NY City TB sanatorium, the City was prepared, the professionals trained and the outbreak controlled. Massive numbers in New York were subject to a plethora of deadly diseases which were handled locally. New York survived. There was no Federal help since it did not exist, it was Harding and Coolidge. 

Yet this author in classic Progressive manners take on the budget cuts as the cause of the problem. The problem arose by what appears to be a deficit in Medical expertise, mistakes, and mishandling. In addition the Federal authorities exacerbated the problem.

This same author continues:

The NIH, which funds important advances in our understanding and treatment of diseases like Ebola, has also suffered cutbacks. Its budget has stagnated for most of the past decade, except for years when it was dramatically reduced, such as in 2013. This has forced productive research laboratories to close, putting potentially life-saving research – like that on an Ebola vaccine – on the back burner.
Now  the problem with Ebola was that it just was not a problem. There were small outbreaks and all generally were controlled. Here in the current situation we have a different problem, one of massive defects in the US system, for which no more money would ever solve. It is akin to just washing one's hands.

This Syndicate piece lacks in my opinion any credibility and just adds more political gasoline to the fire. It is a shame.

Wednesday, October 15, 2014

Microsoft Must Really Hate Its Customers

It appears again that Microsoft demonstrates its contempt for its customers. The issue is a re-release of an update package that results in crashes. A UK Blogger says:

This KB 2952664 update for Windows 7 has been continually pushed out by Microsoft almost every month since April 2014 with various tweaks and revisions. Most have had some degree of install problems or have caused some degree of system instabilities. The October 2014 version appears to be the most problematic. It isn’t needed so don’t install it. It is for reasons like this that I now  recommend NOT to use automatic updates  for windows and do a manual update on 2nd and 4th Tuesdays of the month and check what updates are being installed. Updates are supposed to secure the system and improve it, not cause problems. There have been far too many broken, damaged and unnecessary windows updates forced on a computer recently and it breaks the trust we have with Microsoft updates, that we expect to protect us and only give us automatic  updates we need and that are relevant to the computer.  Updates like this one should be optional and should not ever be pushed down the regular automatic update channel.

 It appears that Microsoft keeps sending out this rather dangerous item and the only solution is as noted above, stop the auto updates and only selectively update.

After the apparent anti-woman outburst by the current CEO one wonders how long this collection of overblown egos will survive.

Remember, if all else fails listen to the customer. This is something that Microsoft has always failed to do.

Tuesday, October 14, 2014

More on SNPs and PCa


The problem often found in examining PCa patients with Gleason 7 lesions is to assess whether they are aggressive or indolent. There has been an explosion of putative markets ranging from SNPs, Genes, promoters, miRNAs, methylations and any combination thereto. We generally understand on a cell by cell basis what is occurring in many malignancies and the logic to such changes. But examining cells in a broad spectrum basis, say from any part of the body, to ascertain what a specific tumor portends is highly problematic. The reason is that

Some researchers have argued that SNPs are highly useful. For example Yonggang et al argue:

A major advantage of using SNP data over microarray data to study genetic predisposition is that, unlike microarray data, a person’s SNP pattern is unlikely to change over time. Loosely stated, the SNP pattern collected from a person with a disease is likely to be the same pattern that would have been collected from that person at birth or early in life. Thus, we can use SNP data from patients at any stage of their life and at any stage of their disease progression.

However there is no fully accepted basis of that assertion. For example if the lesion is initiated by some methylation resulting from some excess inflammation, and the methylation induces some resulting transcription blockage, then the SNP is irrelevant unless it can be expressly shown to be causative. The mechanisms for such are problematic. Admittedly a SNP in a promoter region may demonstrate blockage of the promoter but most likely must do so on both chromosomes.

A second major advantage of using SNP data is that the data can be collected from any tissue in the body. With microarray data, the mRNA samples for cancer patients are taken from tumor tissue (e.g., from the colon), and the mRNA samples for healthy donors are taken from healthy tissue of the same type (e.g., colon again). SNP data, on the other hand, is not taken directly from tumor samples, but from any tissue in the body. The benefit of this is that, in addition to being faster to obtain, SNP data is also easier to obtain since less invasive procedures can be used. On the other hand, when using SNP data, we do not expect to have predictors of as high accuracy as we get with microarray data.

Again one must examine this assertion in detail. Does every cell reflect all others in the body? In PCa for example we know that as the tumor progresses the cells express differently, for example look at PTEN, and also in the case of a PCa stem cell we again may have a substantially different expression.

Thus each time we see a result promoting SNPs we must be somewhat cautious.

For example in a paper by Lin et al we have an interesting and supportive developed in a causative manner. They state:

However, in many disorders including prostate cancer, the balance between stimulators and inhibitors is tilted to favor stimulators, resulting in an ‘‘angiogenic switch’’. The so- called ‘‘angiogenic switch’’ may result from changes in the expression levels of genes in the angiogenesis pathway. Single nucleotide polymorphisms (SNP) in angiogenesis genes may alter gene expression and influence the process of angiogenesis in prostate cancer and inhibited tumor growth in animal models. Indeed, several SNPs in angiogenesis genes that affect gene expression have been identified. These variants may potentially contribute to inter-individual variation in the risk and progression of prostate tumors. Furthermore, angiogenesis is shown to be associated with the Gleason score, tumor stage, progression, metastasis and survival among prostate cancer patients. Although the number of studies for evaluating the role of SNPs in angiogenesis genes is limited, several of the studies support the association between angiogenesis and prostate cancer aggressiveness. So far, results from several candidate gene and genome-wide association (GWA) studies suggest that SNPs in the angiogenesis pathway may be important in prostate cancer progression and aggressiveness.

Here the authors have not only a correlative connection but a causative one, perhaps.
SNPs Again

SNPs are single nucleotide changes in a chromosome. There are millions and the clinical significance is at best problematic. The impact of a SNP on the

As Yonggang et al state:

A significant contribution to the genetic variation among individuals is the cumulative effect of a number of discrete, single-base changes in the human genome that are relatively easy to detect. These single positions of variation in DNA are called single nucleotide polymorphisms, or SNPs. While it is presently infeasible to obtain the sequence of all the DNA of a patient, it is feasible to quickly measure that patient’s SNP pattern – the particular DNA bases present at a large number of these SNP positions.

The statement of SNPs being substantial elements of genetic variation is not all that obvious. We do observe that some clusters of SNP individuals have a higher propensity for a disease but that may be correlative rather than causative.

SNPs can appear anywhere in a chromosome. As shown above they can be in coding regions, non-coding regions and across promoter regions. What are the effects of these changes? That has been a driving question and it is the issue that must be addressed before correlative effects are used.
Recent Reports
In a paper by Yonggang et al they report:

Gleason score (GS) 7 prostate cancer is a heterogeneous disease with different clinical behavior. We sought to identify genetic biomarkers that may predict the aggressiveness of GS 7 diseases.
We genotyped 72 prostate cancer susceptibility SNPs identified in genome-wide association studies in 1,827 white men with histologically confirmed prostate adenocarcinoma. SNPs associated with disease aggressiveness were identified by comparing high-aggressive (GS ≥8) and low-aggressive (GS ≤6) cases. The significant SNPs were then tested to see whether they could further stratify GS 7 prostate cancer.

Three SNPs—rs2735839, rs10486567, and rs103294—were associated with biopsy-proven high-aggressive (GS ≥8) prostate cancer (P < 0.05).

Furthermore, the frequency of the variant allele (A) at rs2735839 was significantly higher in patients with biopsy-proven GS 4+3 disease than in those with GS 3 + 4 disease (P = 0.003). In multivariate logistic regression analysis, patients carrying the A allele at rs2735839 exhibited a 1.85-fold (95% confidence interval, 1.31–2.61) increased risk of being GS 4 + 3 compared with those with GS 3 + 4.

The rs2735839 is located 600 base pair downstream of the KLK3 gene (encoding PSA) on 19q13.33 and has been shown to modulate PSA level, providing strong biologic plausibility for its association with prostate cancer aggressiveness. We confirmed the association of the rs2735839 with high-aggressive prostate cancer (GS ≥8).

The question is how does it modulate the activity and if it does then why does a malignancy occur all too often late in life if that SNP has been sitting there for so long. They continue:

Moreover, we reported for the first time that rs2735839 can stratify GS 7 patients, which would be clinically important for more accurately assessing the clinical behavior of the intermediate-grade prostate cancer and for tailoring personalized treatment and post-treatment management.

In effect the above mentioned SNP, which modulates KLK3 or the PSA gene somehow, can be used as a monitor itself. One could then argue that changes in PSA are reflective of changes in the SNP modulation effect and this have a further basis for continuing PSA measurements.

From NCBI we have the following summary discussing KLK3[1]:

Kallikreins are a subgroup of serine proteases having diverse physiological functions. Growing evidence suggests that many kallikreins are implicated in carcinogenesis and some have potential as novel cancer and other disease biomarkers. This gene is one of the fifteen kallikrein subfamily members located in a cluster on chromosome 19. Its protein product is a protease present in seminal plasma. It is thought to function normally in the liquefaction of seminal coagulum, presumably by hydrolysis of the high molecular mass seminal vesicle protein. Serum level of this protein, called PSA in the clinical setting, is useful in the diagnosis and monitoring of prostatic carcinoma. Alternate splicing of this gene generates several transcript variants encoding different isoforms.

The PSA process is shown below:

The above demonstrates the normal process for PSA production.

From Waltering[2]:

Kallikrein related peptidase 3 (KLK3), better known as prostate specific antigen (PSA), is located in chromosome 19q13.41. KLK3 encodes a single chain glycoprotein with a molecular mass of 33 kDa and functions as a serine protease. It belongs to the family of the fifteen kallikrein members located in a cluster in the same chromosomal region. All kallikrein genes encode five exons of similar size and have high sequence homology with other family members. Many of these peptidases also have several alternative splice variants and are known to be regulated by androgens. KLK3 was cloned in 1987. KLK3 expression has been shown to be elevated in BPH and in highly differentiated PCs, but it is decreased during PC progression.

The use of KLK3 as a PC biomarker (the so-called PSA test) began in the mid-1980s. In a recent European study, which included more than 160,000 men aged 55 to 69; it was found that PSA based screening reduced PC mortality by 20%. However, there was a high risk of overdiagnosis. Androgen regulation of KLK3 includes both the proximal promoter and the enhancer ARE located 4 kb upstream from the TSS. Recruitment of AR and its co-regulators create a chromosomal loop from the enhancer to the core promoter. Kallikrein family members have also been suggested to play a putative role in PC progression. For example, KLK3 has been suggested to directly degrade extracellular matrix glycoproteins and facilitate cell migration.

From a Eureka report on this work they state[3]:

Researchers at The University of Texas MD Anderson Cancer Center have identified a biomarker living next door to the KLK3 gene that can predict which GS7 prostate cancer patients will have a more aggressive form of cancer.

The results reported in the journal of Clinical Cancer Research, a publication of the American Association of Cancer Research, indicate the KLK3 gene – a gene on chromosome 19 responsible for encoding the prostate-specific antigen (PSA) – is not only associated with prostate cancer aggression, but a single nucleotide polymorphism (SNP) on it is more apparent in cancer patients with GS7.

Researchers have linked Gleason score, an important predictor of prostate cancer outcomes, to several clinical end points, including clinical stage, cancer aggression and survival. There has been much research associated with prostate cancer outcomes as well as GS7 prostate cancers, which is an intermediate grade of cancer accounting for 30 to 40 percent of all prostate cancers.

"This is the first report that I am aware of that indicates a genetic variant can stratify GS7 prostate cancer patients," said Jian Gu, Ph.D., associate professor at MD Anderson, and a key investigator on the study. "This is important because this group with heterogeneous prognosis is difficult to predict and there are no reliable biomarkers to stratify this group."

In this study, researchers investigated inherited genetic variants to see if there would be any promising biomarkers for prostate cancer patients. The investigators studied the genetic makeup of 72 SNPs identified from the genome-wide association studies (GWAS) in 1,827 prostate cancer patients. They analyzed associations of these SNPs with disease aggression, comparing them in clinically defined high and low aggressive cases. They found a SNP on the KLK3 gene that can predict an aggressive form of GS7 disease.

"Treatment options for the GS7 disease are controversial because the burden of combined treatment modalities may outweigh the potential benefit in some patients," said Xifeng Wu, M.D., Ph.D., professor and chair of Epidemiology, and lead investigator on the study. "It is critical that we develop personalized treatments based on additional biomarkers to stratify GS7 prostate cancers. Additional biomarkers may help us achieve personalized clinical management of low and intermediate risk prostate cancer patients."

Wu also said her team are expanding the study and taking a pathway-based approach to systemically investigate genetic variants in microRNA regulatory pathways as biomarkers for the prognosis of prostate cancer patients. "We are also working on circulating biomarkers. Eventually, we will incorporate all biomarkers, epidemiological and clinical variants into nomograms to best predict the prognosis of prostate cancer patients at diagnosis."

Now many others have studies SNPs and PCa[4]. In a recent paper by Mikropoulos et al on Medscape the authors provide an excellent up to date summary[5]:

Several SNPs associated with PrCa risk in the 8q24 locus were among the earliest identified. The 8q24 region is a gene-poor region located upstream of the MYC proto-oncogene and this suggested an association with its expression, which was later proven to occur in a tissue-specific manner. Another important SNP is rs10993994 in the region containing the MSMB gene on chromosome 10. This risk allele associates with reduced MSMB protein expression. MSMB expression is high in normal and benign prostate tissue and low in PrCa. MSMB regulates cell growth and when lost, tumor cells grow in an uncontrolled manner. The odds ratio (OR) for this SNP's association to PrCa was established as 1.61. This is a potential biomarker since urine MSMB assays have been developed and their role in screening is being evaluated.

The Myc region is always a sensitive region. Myc controls cell proliferation and as such needs close control. They continue:

SNP rs2735839 was identified between the KLK2 and KLK3 genes on chromosome 19 where there is a kallikrein gene cluster. Kallikreins are serum proteases and the most well-known member of this group is the prostate-specific antigen (PSA), which is widely used for screening and monitoring PrCa. SNPs were also identified in the intronic region areas of the LMTK2 gene, which codes for cdk5, the SLC22A3 gene, which codes for an organic cation transporter and NUDT10, which regulates DNA phosphorylation.

Again the proximity to PSA gene expression is noted. This has been the case for many previous works not just the one we have focused on herein.

In proximity to the TERT gene (encoding TERT) on 5p15, a further susceptibility SNP was identified (rs2242652). Telomerase is important in counterbalancing telomere-dependent replicative aging. SNPs in this region have been associated with numerous cancers, such as basal cell carcinoma, lung cancer, bladder cancer, glioma and testicular cancer. This SNP showed an association with high PSA levels, as well as increased risk of developing PrCa. Fine-mapping analysis identified a total of four loci independently associated with PrCa risk in the TERT region, one of which was associated with changes in gene expression.

rs2121875 is a SNP located at 5p12 within the FGF10 locus associated with an increased risk of PrCa. FGF10 is often overexpressed in breast carcinomas, and encodes a FGF essential for a range of developmental processes, which also has an important role in the growth of normal prostatic epithelial cells.

In 2013, we reported on 23 new susceptibility alleles associated with PrCa, 16 of which were also associated with aggressive disease.. A SNP located at 1q32 (rs4245739) in proximity to the MDM4 gene is of potential clinical significance. MDM4 inhibits cell cycle arrest and apoptosis, via p53 downregulation.[30] Another SNP (rs11568818) with a potential prognostic value is situated at 11q22 within a region containing the gene MMP7. MMP7 encodes for a matrix metalloproteinase, which is pivotal for tumor metastasis and overexpression of MMP7 is a potential biomarker for PrCa aggressiveness and risk of metastatic disease. Finally, SNP (rs7141529) at 14q24 is an intronic SNP within the RAD51B gene, which is an important DNA repair gene involved in homologous recombination, also associated with PrCa risk.

From this report we also present below the detailed tabular results on a wide variety of SNPs.

Nearby gene
Gene function
Calmodulin binding
MDM4 and PIK3C2B
Negative TP53 regulator and therefore inhibits cell cycle arrest and apoptosis and positive regulation of cell proliferation
SNARE interactions in vesicular transport
Intronic in EHBP1
Eps15 homology domain binding protein
Intronic in THADA
Complex locus
Catalytic activity
TBP-associated factor
Intronic in ITGA6
Integrins-cell adhesion cell surface-mediated signaling
Exophilin subfamily of Rab effector proteins
Rac protein signal transduction


Intronic in EEFSEC
GTP binding, GTPase activity, nucleotide binding, translation elongation factor activity
Intronic in ZBTB38
Transcriptional activator that binds methylated DNA
CNS myelin
Structurally-related serum transport proteins
Intronic in PDLIM5
Cytoskeleton organization, cell lineage specification and organ development oncogenesis

Metal ion binding, oxidoreductase activity
Important role in the growth of normal prostatic epithelial cells
Telomerase is important in counterbalancing telomere-dependent replicative aging
Regulation of transcription, DNA dependent
Encoding biorientation of chromosomes in cell division 1
Missense coding in CCHCR1
Protein binding
FOX transcription factor family
Notch signaling network
RFX family of transcription factors
Intronic in SLC22A3
Cation transporter gene

Intronic in JAZF1
Transcriptional repressor
Transcription factor
Intronic in LMTK2
Tyrosine kinase
Mitochondrial carrier proteins
Homeodomain-containing transcription factor NKX3–1
Regulation of transcription
c-MYC oncogene
Transcription factor activity controlling cell cycle progression, apoptosis and cellular transformation






Intronic in DAB2IP
GAP tumor suppressor
Nucleotide excision repair
Ras GAP tumor suppressor
MSMB gene
MSMB regulates cell growth
Ligase activity
Intronic in CTBP2
Wnt signaling pathway and Notch signaling pathway



Matrix metalloproteinase associated with metastatic potential
Cellular structural integrity
Protein binding, GTP binding, GTPase activity, nucleotide binding and structural molecule activity
Transcription factors involved in the regulation of developmental processes

Actin cytoskeleton organization, cell adhesion, regulation of cell shape
DNA repair
VPS53 and FAM57A
Protein transport
Transcription regulation
Encoding transcription factor homeobox B13
Intronic in HNF1B
Homeodomain-containing superfamily of transcription factors


Regulation of transcription
KLK2 and KLK3 regions
Serine proteases


Immunoreceptors expressed predominantly on monocytes and B cells

Transmembrane adaptor phosphoprotein
Cyclin-dependent protein kinase regulator activity
Amiloride-sensitive sodium channel activity beta-catenin binding
Diphosphoinositol-polyphosphate diphosphatase activity, hydrolase activity and metal ion binding
Androgen receptor
Androgen receptor regulation


This paper that we have been discussing presents a SNP analysis which has some logical nexus to PSA and pathways often found aberrant in PCa. We are left asking a few questions:

1. What is the controlling mechanism between the SNP and the PSA production?

There seems at best closeness to PSA and an argument that the proximity is reflective of the aggressiveness of the malignancy. There must be a clearer understanding of the entire process before arguing as is done above.

2. Why if the SNP is in the gene does it not cause a PCa effect earlier? What then is the precipitating sequence of events?

This is the key question. If these SNPs are pandemic in all cells then why is PCa specific and why does it take so long? What is truly occurring here?

3. What are the pathway effects?

There appears to be a great deal of inferential data but no clear definitive linkages. The problem with SNPs all too often is the correlative and non-causative relationships.

4. Can one examine a means to block the deleterious effects of this modulation and if so what are they?

This is the therapeutic question. Again one needs the details and not just single nucleotide suggestions.

5. How cell specific is this SNP and as we have seen, many SNPs have broader imputed effects.

We have examined many of the ROC curves and they are interesting but not conclusive. One may not want to bet one’s patient’s lives on these specific markers


Lin , H. et al, SNP-SNP Interaction Network in Angiogenesis Genes Associated with Prostate Cancer Aggressiveness, PLOS ONE, www.plosone.org , April 2013, Volume 8, Issue 4
Waddell, M., et al, Predicting Cancer Susceptibility from Single-Nucleotide Polymorphism Data: A Case Study in Multiple Myeloma, BIOKDD ’05, August 2005.
Waltering, K., Androgen Receptor Signaling Pathway in Prostate Cancer, PhD Thesis, Univ Tampere, Sept 2010.
Yonggang, H., et al, The Prostate Cancer Susceptibility Variant rs2735839 Near KLK3 Gene Is Associated with Aggressive Prostate Cancer and Can Stratify Gleason Score 7 Patients, http://clincancerres.aacrjournals.org/content/20/19/5133.abstract