Fresh Pond Research Institute

This paper describes the computer program, l\_bnl\_compress.py. which is a Python script implementing the lossy compressions described in Bernstein, H. J., Soares, A. S., Horvat, K. & Jakoncic, J. (2024). J. Sync. Rad. 32(2) for macromolecular crystallographic diffraction data. The lossy compressions use pixel-by-pixel binning, image-by-image summing, JPEG-2000 Daubechies (DB) wavelet compression from the movie industry, and HCompress Haar (now known as DB0) wavelet compression from astronomy which are combined with the usual lossless MX compressions.

Since 2014 SAUC1 has provided a search engine to find crystallographic unit cells similar to a given probe cell. The data for the version available on the LRL_WEB, Lattice Representation Library Tool Web Page2, has been updated to report on 191,000 Protein Data Bank macromolecular unit cells and 434,000 small molecule unit cells from the Crystallography Open Database for a searchable database of over 625,000 small molecule and macromolecular unit cells. The update was done in February 2025. The search copes well with complex boundary cases and will be updated approximately semi-annually.A sample of a search for the cells in the vicinity of the chymotrypsinogen cell from PDB entry 7KTY3 is attached.

We use both lossy and lossless compression methods to reduce large amounts of digital data, making it easier to store and manage. Lossy and lossless compression is frequently used in astronomy, to condense the large amount of data collected by instruments namely, the James Webb Space Telescope and the Hubble Space Telescope. Similarly to diffraction images, astronomical images have large areas of empty space since stellar objects are very bright, yet show very small in images, which after a while, takes up a needless amount of limited digital storage space. Lossy compression achieves higher compression ratios but sacrifices some data quality in the process, while lossless compression preserves the data’s original form, but results in less storage savings. This work, conducted at Brookhaven National Laboratory’s National Synchrotron Light Source-II at the AMX and FMX macromolecular beam lines, aimed to evaluate the effectiveness of the lossy compression method known as Wavelet Compression. Wavelet compression is a method of data compression that uses wavelet transforms to reduce the size of data while preserving its essential features. Crystals are repetitive molecular assemblies that create diffraction patterns when exposed to X-rays, while detectors capture the amplitude of diffraction pattern spots (reflections). Similar to astronomical images, diffraction images contain large areas of empty space. This unnecessary data can quickly consume limited digital storage. By studying and optimizing compression methods, we not only improve data management but also advancements in various scientific disciplines.

How many human embryos die between fertilisation and birth under natural conditions? It is widely accepted that natural human embryo mortality is high, particularly during the first weeks after fertilisation, with total prenatal losses of 70% and higher frequently claimed. However, the first external sign of pregnancy occurs two weeks after fertilisation with a missed menstrual period, and establishing the fate of embryos before this is challenging. Calculations are additionally hampered by a lack of data on the efficiency of fertilisation under natural conditions. Four distinct sources are used to justify quantitative claims regarding embryo loss: (i) a hypothesis published by Roberts & Lowe in The Lancet is widely cited but has no practical quantitative value; (ii) life table analyses give consistent assessments of clinical pregnancy loss, but cannot illuminate losses at earlier stages of development; (iii) studies that measure human chorionic gonadotrophin (hCG) reveal losses in the second week of development and beyond, but not before; and (iv) the classic studies of Hertig and Rock offer the only direct insight into the fate of human embryos from fertilisation under natural conditions. Re-examination of Hertig’s data demonstrates that his estimates for fertilisation rate and early embryo loss are highly imprecise and casts doubt on the validity of his numerical analysis. A recent re-analysis of hCG study data concluded that approximately 40-60% of embryos may be lost between fertilisation and birth, although this will vary substantially between individual women. In conclusion, natural human embryo mortality is lower than often claimed and widely accepted. Estimates for total prenatal mortality of 70% or higher are exaggerated and not supported by the available data.

Summary Our understanding of the evolution of sex ratios has advanced substantially in recent decades, in part due to the important work of Hamilton (1967) on ‘extraordinary sex ratios’. However, important aspects of the biology have largely remained unstudied, including the mating dynamics and structure of natural populations, the role of the individual in producing observed sex ratios, and the nature of sex ratio control. Also little studied is how tests of sex ratio models should be structured so as to provide maximum insight. Perhaps ignoring these facets of the biology has aided progress in the past, but these gaps in the study of sex ratios are now blindspots, which hinder understanding. Further progress in the evolutionary analysis of sex ratios requires their elimination. This can be accomplished only by direct investigations of mating dynamics, population structure and the behaviour of individuals. Introduction Every great scientific theory is a partial lie about nature. This is not a claim about scientific fraud, as the issue is not one of honesty in the usual sense. Instead, it is a claim about how theories succeed (Cartwright 1984). A theory can succeed by explaining facts correctly. It can also succeed by making facts appear irrelevant or unimportant, sometimes correctly but sometimes incorrectly. Such facts sometimes resurface, but sometimes they are never seen again (Lewontin 1991). To this extent, the lie arises because nature is not described, as much as it is created from some facts while others are eliminated and left unexplained.

In the Philosophical Investigations, Wittgenstein (1968, 94) describes a man who is unconvinced by a claim he reads in a newspaper, so he buys another copy of the same newspaper to double-check. The point of the joke is that it isn't just the quantity of evidence in support of a claim that matters, but the quantity of independent evidence (Sober 1989).