98% of our DNA has until recently been considered "junk." That's the percentage that's not devoted to recipeing proteins, which for decades was supposed to be what DNA was all about. But the view of so-called junk DNA has been slowly changing. Better tools and procedures have allowed researchers to locate mutations implicated in rare genetic diseases, and many of these mutations turn out to be located in the "junk" areas. As clues mount, scientists can start connecting dots and developing theories regarding multitudes of previously unconsidered ways in which genetic errors can cause problems.

Ms. Carey's book does not make many generalizations about junk DNA's overall purposes might be. Instead she relates disparate tales of research results as relating to known genetic disorders. Her stories exemplify the strange, non-intuitive ways that genetic information can interact. It doesn't seem likely that science will soon have an orderly story to tell about how it all works.

Many of the interactions are actually epigenetic rather than genetic, meaning that they concern markers added to the the genetic code rather than the code itself. Epigenetic markings can be prompted by changes in the cell environment. Their purpose is to enable, amplify, damp down, or turn off individual genes. Their role and presence vastly complicates the whole genetic picture. Richard Dawkins's view of genes as simple, coherent actors seems increasingly naive.

This book is well and entertainingly written, but may be too technical for some readers. Something of a refresher course in cell biology might be advisable before giving this a go. ( )

Phew! I've finally finished this book. Not to put too fine a point on it: it has been a hard slog. The field of genetics is just becoming so complex as more and more of the chemistry is unravelled. This particular book focuses on the role of "junk DNA" .....the stuff that seems randomly inserted in our genetic DNA but doesn't actually code for proteins. Over 98 percent of the DNA in a human cell is junk!. It doesn't code for any proteins. When I studied genetics ......hmm 56 years ago the big news was the Watson Crick model of DNA. And, as I recall, the great new advances were in unravelling the role of messenger RNA. I remember hating the mathematical/statistical stuff that we had to absorb about gene swapping in maize.
Clearly, a lot has happened since then. But the sheer size of the genome and the complexities introduced by the processes: mitosis, meiosis, gene duplication, messenger RNA, transfer RNA, gene expression, gene inhibition, molecular geometry, proteins as enzymes, the environment .....and now junk DNA. It really comes as no great surprise that the long stretches...and small stretches of amino acids that don't code for proteins are not all there by accident. They are not all remnants of some long lost symbiont or virus. Many of them have major roles in "telling" genes when to switch on and when to switch off; when to express a function and when to inhibit it.......kind of the laws and protocols for the genes.
Nessa Carey has the rare gift of being able to use colourful analogies to explain complex behaviour ...though it's not without its limits. For example, she conjures up the picture of a velcro-gloved piano player who's fingers get attached to certain keys but they also get random fluff on the back. I found myself asking ..what fluff? where does the fluff come from? And there were a few instances of this. She also includes a lot of helpful diagrams though in many cases, where the prose becomes overwhelming, I was wishing she had included a lot more...and colour would be a big help. And there are many sections where the prose IS overpowering and just too complex...eg p230 talking about Myotonic dystrophy. Also, because the field is littered with its own terminology we seem to have new terms introduced (which are clearly the everyday language of the epigeneticist) that either seem strange or confusing ...but, anyway, they really need definition and a glossary would have helped me a lot. For example she seems to introduce the term "titration" p231 ..which doesn't seem to have any connection with the titration that I'm familiar with in the laboratory, she also introduces the word "motif" ...which I take refers to a group of amino acids ...but it's not clear to me...and there were other terms that I struggled with even where they may have been defined earlier in the book. Often they were used later in the book and the index was of no help in locating the word....so, a better index needed too.
Most of the effects of junk DNA appear to be demonstrated by a bewildering array of genetic diseases ...and rather depressing reading it is too. I found myself wondering whether genetic testing of the parents and of the embryo, combined with knowledge of the likely problems of a baby born with these "defects" ....and the subsequent impact on the parents etc. and the ability to abort ....might be a better way of dealing with these issues than trying to devise drugs that don't really solve the underlying mutations etc. After all, that is more or less the evolutionary pathway anyway: non-helpful mutations get weeded out ...they don't get to reproduce. Isn't this eugenics? Well only up to a point and it could save a lot of pain and heartache...and maybe deliver the greatest good for the greatest number.
Did I learn anything? Well yes; I learned a lot...just don't ask me to explain it all to you. I think I might have to read this several times to try and take in all the mechanisms that Nessa talks about...but life is too short.
Here is a grab bag of the different "expressions" of junk DNA that she talks about:
1. An expanded length within junk prevents the RNA from making messenger RNA
2. Over 40% of the human genome is composed of "foreign interlopers" (Maybe transferred in by viruses or bacteria etc) and they have duplicated themselves ("repeats") ...the majority of the repeats occurred 125M years ago before placental mammals separated from other lineages. But have been decreasing in primates.......so less of a cause for genetic mutations in humans than in mice. And these repeats can cause problems when crossing over occurs.
3. The chromosomes have ends ...the telomeres....which are made up of junk DNA. If we didn't have these the DNA repair machinery would join up the strands of DNA. But the telomere DNA doesn't keep getting renewed and they get shorter over time and are related to (or cause of) ageing.
4. The centromeres are made up of junk DNA .....they act as a binding site for the CENP-A protein ...this gives the spindle something to hang on to.

Carey follows up her book on epigenetics (essentially the effects of parts of DNA that aren't the base-pairs that make up genes) with another that looks at the 98% of your DNA that doesn't code for proteins, generally referred to as "junk" because it was believed it had no biological function.

This model, that all you need to understand cellular life is a list of the protein-coding segments of DNA, has completely colapsed. Numerous DNA sequences that have nothing directly to do with protein manufacture have been found to be essential to the proper functioning of cells in complex life. You can learn about many of them here, in a very clear, fair and balanced way.

I have become interested in the actual chemistry of the various processes Carey describes in her first two books at the level of metaphor. I'm not sure where to find out about that, short of an academic text. Similarly, although the references to the academic literature are all present and correct, Carey glosses over the details of the experiments used to reach the conclusions expressed. A book about that would go down well, too.

Carey has a book about gene editing and CRISPR - I'm looking forward to reading that, too. ( )

Junk DNA: A Journey Through the Dark Matter of the Genome discusses the uses and functions of the 98% of DNA that doesn't code for a specific protein (i.e. "Junk DNA"). The topics covered in this book include retrogenes, DNA/RNA repeats, protein sequences, non-protein coding RNAs, telomeres, enhancers, promoters, epigenetics, 3D interatctions, splicing, insulators, centromeres and examples of the various diseases and disorders that can occur when "junk DNA/RNA doesn't function properly. The information covered in the book is very interesting and mostly easy to understand for the non-scientist and non-genetic specialist. There is a fair amount of technical detail, but it is impossible not to have technical details in a book that discusses the biochemistry of cell function and DNA expression. The inclusion of illustrative analogies and diagrams helps the reader picture the cellular functions and concepts. A rather nice overview of a complex subject.



NOTE: Author has irritating habit of insisting that the human appendix has no useful function and is a relic of evolution. This is an outdated idea. For those interested, the appendix:.
(1) functions as a safe-haven for useful/friendly bacteria when illness flushes those bacteria from the rest of the intestines.
(2) has more recently been identified as an important component of mammalian mucosal immune function. The appendix helps in the proper movement and removal of waste matter in the digestive system, contains lymphatic vessels that regulate pathogens, and might even produce early defences that prevent deadly diseases.

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