Best biochemistry books according to redditors
We found 268 Reddit comments discussing the best biochemistry books. We ranked the 131 resulting products by number of redditors who mentioned them. Here are the top 20.
We found 268 Reddit comments discussing the best biochemistry books. We ranked the 131 resulting products by number of redditors who mentioned them. Here are the top 20.
Finally there's a question that's my exact field.
Proteins are huge macromolecules made of a linear arrangement of amino acids that is folded in 3D. The one I'm studying is about 70,000Da, so about the mass of 70,000 hydrogen molecules. It's composed of ~609 amino acids, which are fairly complex molecules themselves. Here is an amino acid. Here's a short peptide sequence composed of 4 amino acids. This looks pretty simple, but imagine 600 in a row. There are 20 different "R" groups which makes it more complex. There are two angles that can rotate freely, phi (NH to alpha carbon) and psi (alpha carbon to carbonyl carbon). Diagram of these angles here. So you have a huge linear molecule that folds in hundreds of places and all the atoms can interact with each other.
To get a 3D image, a protein must be crystallized, meaning it has to from a regular lattice structure. This is very hard to do. You need to isolate your protein very well and have rather large quantities of it because you never know which solution will work. First you have to get it started (nucleation) and get additional proteins to join in. I won't get in to how this occurs but it often involves cat whiskers. It's pretty much an art. Then, once you have a crystal structure, you beam it with x-rays, and predict the structure by how the x-rays are diffracted. You often don't get a good "view" of what's on the inside of the protein. Here are 3 representations of a small and simple protein.
Folding@Home predicts the structure without having to do this long and difficult to achieve process. You have to account for favorable and unfavorable interactions and bond angles and are able to achieve a good estimation of the structure.
EDIT: If you're interested, here's a good 17 minute video on x-ray crystallization. I've been working towards crystallization of my protein for 5 months and still have a ways to go.
EDIT2: Reading more about F@H, I learned that it also aims to find insight in to how proteins fold. This is still a mystery to us. An unfolded protein has an astronomical number of possible conformations. Cyrus Levinthal calculated that if a completely unfolded protein is composed of 100 amino acids, there are 10^143 possible. If each conformation is "tried out" by a protein for a millisecond, it would take longer than the age of the universe to try them all. I'm sorry but I'm very busy tonight and can't get that deep into protein folding, but we do know that it starts with a nucleation (here it means you first form a very stable part of the protein) and then the the more unstable parts form but it is still largely a mystery. What makes it even tougher is that the most stable conformation is not always the native/active one. Also, Structure and Mechanism in Protein Science by Alan Fersht is a very good book for biochemists and is what I use as a desk reference.
I'll stick to recommending science communication books (those that don't require a deep background on biological concepts):
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For books that everyone studying biology ends up reading, my candidate would be Lehninger's Principles of Biochemistry, by Nelson & Cox but that's a textbook.
LMAO
>Peterson:
>I read The Cosmic Serpent, by Jeremy Narby (https://amzn.to/2J2IklU) and found it interesting. It's far from obvious what people can and can't see under the influence of psychedelics. And I didn't "claim" anything. I put forward a tentative hypothesis. That is by no means a claim. If you have a better idea, put it forward.
>/u/BBDG
>From your lecture: ?>https://twitter.com/zei_nabq/status/997575537089564672/video/1
>I really believe that's a representation of DNA
Not exactly concrete, but several years ago I read a book called The Cosmic Serpent: DNA and the Origins of Knowledge.
The name of this thread reminded me of it, and I came here to share the recommendation with anyone interested.
Long story short (please read the book if you're interested) an anthropologist goes into South America, connects with a disconnected remote tribe, begins to study their... well, everything.
For instance, Ayahuasca has an extremely complex preparation procedure, involving a root from one and bark of another plant, combinations of drying and heating, etc. and if the process is not properly completed, you can end up with a toxic brew instead of your hallucino-spirit drug.
When our author would ask how they came to such a complex and seemingly random process, the shaman told him "The plants told us."
He starts to take such answers at face value, and draws some very interesting and awesome theories. The book is a great read, especially for a skeptic.
Relevant: The paintings and art of the shaman this particular anthropologist was involved with were very, very clearly (in some instances) depictions of micro-biological constructs. Here a mitochondria, there a cell wall, here some proteins, etc.
The ultimate "theory" posed by the book involves the idea that DNA is a language commonly "spoke" by all living organisms, and that there are ways to tap into that level of language to communicate on a more literal level.
Not... concrete, but still very interesting, and scientific in nature. :)
Chemistry has some expensive textbooks (each separate word is its own link)
Excerpt from my biochemistry text - identical twins have much higher rates of both developing type 2 than type 1.
Type 1 vs Type 2 comparison chart
Other generic Type 1/Type 2 information
All from this textbook http://www.amazon.com/Biochemistry-Lippincott-Illustrated-Reviews-Series/dp/1451175620
That hardly seems like an unbiased book. The problem with books like that is that even greatly sourced books, can still use random data to conclude wacky things, like information bouncing off of DNA crystals as the origin of knowledge in the form of a pair of serpants. (Interesting book by the way. The guy is crazy, but a fun kind of crazy).
Here is an actual, scientific study (link stolen from another redditor on another thread).
Mechanisms? You're talking about selection, mutation, genetic drift, gene expression/regulatory evolution, chromosomal inversions/deletions/translocations, TE activity, gene duplication, chromosomal duplication, codon bias, and more. The field is massively broad and encompasses everything from population genetics, to molecular biology, to genomics, to phylogenetics/molecular evolution.
I'm a evolutionary genetics PhD, and there's no review broad enough to cover it all. Maybe narrow it down a bit? Popular(ish) science books may be the thing you're looking for.
For example, this book by Michael Lynch would be a good start. He loves to look at the big picture stuff and tends towards comparative evolutionary genomics. For the soap-opera-like beginnings to population genetics (which really is the central theoretical core of evolutionary genetics), this book by William Provine is an entertaining and enlightening read.
Edit: Gene duplication is a favourite of mine: These authors are good for this review article. I haven't read it myself yet (I'm at home and cannot access it) but if it's published in Nature Reviews Genetics then it's probably very high quality.
Google Scholar is your friend. Search for "gene duplication review" and narrow by year to include more up-to-date. You can use the keywords at the start of my post to get searching.
Here's a list of books I've read that have had a big impact on my journey.
First and foremost tho, you should learn to meditate. That's the most instrumental part of any spiritual path.
Ram Dass – “Be Here Now” - https://www.amazon.com/Be-Here-Now-Ram-Dass/dp/0517543052 - Possibly the most important book in the list – was the biggest impact in my life. Fuses Western and Eastern religions/ideas. Kinda whacky to read, but definitely #1
Ram Dass - “Journey Of Awakening” - https://www.amazon.com/dp/B006L7R2EI - Another Ram Dass book - once I got more into Transcendental Meditation and wanted to learn other ways/types of meditation, this helped out.
Clifford Pickover – “Sex, Drugs, Einstein & Elves…” - https://www.amazon.com/Sex-Drugs-Einstein-Elves-Transcendence/dp/1890572179/ - Somewhat random, frantic book – explores lots of ideas – planted a lot of seeds in my head that I followed up on in most of the books below
Daniel Pinchbeck – “Breaking Open the Head” - https://www.amazon.com/Breaking-Open-Head-Psychedelic-Contemporary/dp/0767907434 - First book I read to explore impact of psychedelics on our brains
Jeremy Narby – “Cosmic Serpent” - https://www.amazon.com/Cosmic-Serpent-DNA-Origins-Knowledge/dp/0874779642/ - Got into this book from the above, explores Ayahuasca deeper and relevancy of serpent symbolism in our society and DNA
Robert Forte – “Entheogens and the Future of Religion” - https://www.amazon.com/Entheogens-Future-Religion-Robert-Forte/dp/1594774382 - Collection of essays and speeches from scientists, religious leaders, etc., about the use of psychedelics (referred to as Entheogens) as the catalyst for religion/spirituality
Clark Strand – “Waking up to the Dark” - https://www.amazon.com/Waking-Up-Dark-Ancient-Sleepless/dp/0812997727 - Explores human’s addiction to artificial light, also gets into femininity of religion as balance to masculine ideas in our society
Lee Bolman – “Leading with Soul” - https://www.amazon.com/Leading-Soul-Uncommon-Journey-Spirit/dp/0470619007 - Discusses using spirituality to foster a better, more supportive and creative workplace – pivotal in my honesty/openness approach when chatting about life with coworkers
Eben Alexander – “Proof of Heaven” - https://www.amazon.com/Proof-Heaven-Neurosurgeons-Journey-Afterlife/dp/1451695195 - A neurophysicist discusses his near death experience and his transformation from non-believer to believer (title is a little click-baity, but very insightful book. His descriptions of his experience align very similarly to deep meditations I’ve had)
Indries Shah – “Thinkers of the East” - https://www.amazon.com/Thinkers-East-Idries-Shah/dp/178479063X/ - A collection of parables and stories from Islamic scholars. Got turned onto Islamic writings after my trip through Pakistan, this book is great for structure around our whole spiritual “journey”
Whitley Strieber – “The Key: A True Encounter” - https://www.amazon.com/Key-True-Encounter-Whitley-Strieber/dp/1585428698 - A man’s recollection of a conversation with a spiritual creature visiting him in a hotel room. Sort of out there, easy to dismiss, but the topics are pretty solid
Mary Scott – “Kundalini in the Physical World” - https://www.amazon.com/Kundalini-Physical-World-Mary-Scott/dp/0710094175/ - Very dense, very difficult scientific book exploring Hinduism and metaphysics (wouldn’t recommend this for light reading, definitely something you’d want to save for later in your “journey”)
Hermann Hesse – “Siddartha” - https://www.barnesandnoble.com/w/siddhartha-hermann-hesse/1116718450? – Short novel about a spiritual journey, coming of age type book. Beautifully written, very enjoyable.
Reza Aslan - “Zealot” - https://www.amazon.com/ZEALOT-Life-Times-Jesus-Nazareth/dp/140006922X - Talks about the historical Jesus - helped me reconnect with Christianity in a way I didn’t have before
Reza Aslan - “No god but God” - https://www.amazon.com/god-but-God-Updated-Evolution/dp/0812982444 - Same as above, but in terms of Mohammad and Islam. I’m starting to try to integrate the “truths” of our religions to try and form my own understanding
Thich Nhat Hanh - “Silence” - https://www.amazon.com/Silence-Power-Quiet-World-Noise-ebook/dp/B00MEIMCVG - Hanh’s a Vietnamese Buddhist monk - in this book he writes a lot about finding the beauty in silence, turning off the voice in our heads and lives, and living in peace.
Paulo Coelho - “The Alchemist” - https://www.amazon.com/Alchemist-Paulo-Coelho/dp/0062315005/ - Sort of a modern day exploration of “the path” similar to “Siddhartha.” Very easy and a joy to read, good concepts of what it means to be on a “path”
Carlos Castaneda - "The Teachings of Don Juan" - The Teachings of Don Juan: A Yaqui Way of Knowledge https://www.amazon.com/dp/0671600419 - Started exploring more into shamanism and indigenous spiritual work; this book was a great intro and written in an entertaining and accessible way.
Jean-Yves Leloup - “The Gospel of Mary” - https://www.amazon.com/Gospel-Mary-Magdalene-Jean-Yves-Leloup/dp/0892819111/ - The book that finally opened my eyes to the potentiality of the teachings of Christ. This book, combined with the one below, have been truly transformative in my belief system and accepting humanity and the power of love beyond what I’ve found so far in my journey.
Jean-Yves Leloup - “The Gospel of Philip” - https://www.amazon.com/Gospel-Philip-Magdalene-Gnosis-Sacred/dp/1594770220 - Really begins to dissect and dive into the metaphysical teachings of Christ, exploring the concept of marriage, human union and sexuality, and the power contained within. This book, combined with the one above, have radically changed my perception of The Church as dissimilar and antithetical to what Christ actually taught.
Ram Dass - “Be Love Now” - https://www.amazon.com/Be-Love-Now-Path-Heart/dp/0061961388 - A follow-up to “Be Here Now” - gets more into the esoteric side of things, his relationship with his Guru, enlightenment, enlightened beings, etc.
Riane Eisler - “The Chalice and the Blade” - https://www.amazon.com/Chalice-Blade-Our-History-Future/dp/0062502891 - An anthropoligical book analyzing the dominative vs cooperative models in the history and pre-history of society and how our roots have been co-opted and rewritten by the dominative model to entrap society into accepting a false truth of violence and dominance as “the way it is”
For pleasure:
Undergraduate
Organic Chemistry as a Second Language, The art of writing reasonable organic reaction mechanisms
Graduate
Due to non-existent biology background, you could start by reading Campbell Biology and Alberts Molecular Biology of the Cell.
CLRS for algorithms/CS.
Probability and random processes for statistics.
Biological Sequence Analysis by Richard Durbin for my subfield of bioinformatics.
I have
The Manga Guide to Molecular Biology https://www.amazon.com/dp/1593272022/ref=cm_sw_r_cp_apa_LF8IBbBB36AGE
And
The Manga Guide to Biochemistry https://www.amazon.com/dp/1593272766/ref=cm_sw_r_cp_apa_RG8IBbHC98RQV
It's sort of like a Dummies book that walks you through some of the concepts.
This is a good answer and true in most forms of life. But as a microbiologist, I need to jump in and point out that prokaryotes do not have histones. The concept is the same, just without those extra proteins for neatly packaging the DNA.
For further reading try Molecular Genetics of Bacteria by Snyder/Champness (Amazon link to most recent version which now has other authors added: https://www.amazon.com/Molecular-Genetics-Bacteria-Larry-Snyder/dp/1555816274 ). This is a comprehensive text that focuses on prokaryotic DNA. Try asking your library for a copy or if you are a teacher/TA buy your own as a good reference text!
Anything by Feynmann are great reads. For upper division instrumental analysis, spectroscopy, and quantum I wholly recommend QED: The Strange Theory of Light and Matter by Richard P. Feynman et al. It describes all the concepts in the book in layman's terms in a brilliant narrative of chemistry. I recommend it to anyone that wants to learn about the strangeness of physics and chemistry. It is easy to digest.
The Feynman Lectures on Physics, although pricey helped me survive physics (I have the paperbacks). It seems you can read the entirety online at that site.
If you choose to do a lot of organic chemistry laboratory work then Advanced Practical Organic Chemistry is a really great resource. It covers just about everything you need to know to be very competent and safe in the lab. I found a used copy of the second edition that has served me well. I don't know what has been updated in the third edition.
I agree with /u/lmo2th Pauling has written albeit old but definitive books on chemistry. Although it can be very difficult to read and knowledge of differential equations is required, Introduction to Quantum Mechanics with Applications to Chemistry by Linus Pauling et al. was the most succinct book on the nitty gritty math of QM I found.
I recently graduated with a B.S. in Chemistry, it was difficult, but I loved every minute I spent in the lab doing research and can't imagine doing anything else. Edit: QED and Feynmann Lectures are great reads for lower division classes. Save the second two for if you decide on chemistry.
"Biological sequence analysis" by Durbin, Eddy, Krogh and Mitchison:
https://www.amazon.com/Biological-Sequence-Analysis-Probabilistic-Proteins/dp/0521629713
also this paper by Krogh et al. might be useful:
https://pdfs.semanticscholar.org/0f88/43d140cb3b3c14afdbe0486b27d2f1016eb3.pdf
and this HMM tutorial by Rabiner:
http://www.ece.ucsb.edu/Faculty/Rabiner/ece259/Reprints/tutorial%20on%20hmm%20and%20applications.pdf
Since you didn't say what exactly you wanted a source for, and just told me to shut up, I'm not sure what exactly you want me to provide. There are a lot of physiology and biochemistry texts to which I can refer you if you'd like to read up on fructose, insulin, and leptin, as these are basic physiological principles. Boron and Boulpaep's Medical Physiology and Lehninger's Principles of Biochemistry are good ones. The nutrition information is also pretty basic. Here's a list of the fructose content of fruits and here's an article from the American Journal of Nutrition discussing the different forms of HFCS, its chemistry, and some of the science around it.
As for the chemistry of fructose as it relates to HFCS, here is a good article from the journal Nutrition and Metabolism, Fructose metabolism in humans – what isotopic tracer studies tell us, that gives a really nice overview of the physiology and biochemistry of fructose. It also does a review of the literature surrounding the purported role that HFCS plays in the obesity problem in the western world. However, one might be inclined to dismiss the article, as it is written by scientists employed by ADM. It's fair to raise this as a possible conflict of interest for the review part of the article. The first part, though, that discusses fructose metabolism, is "morally neutral" -- it doesn't say anything good or bad about fructose, just what happens to it and what they learned from tracer studies.
Given that one could question the review part of the previous article, here are a few other recent articles about fructose and HFCS:
A meta-analysis from 2014 that found no link between increased consumption of sugar of any kind and non-alcoholic liver disease: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4135494/
A double-blind study from 2015 that interestingly found that ingestion of fructose or sucrose-sweetened beverages led to increased food consumption, but that ingestion of aspartame-sweetened beverages did not lead to excess food consumption: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4658464/
The title of this randomized, double blind study from 2016 speaks for itself: Fructose Containing Sugars at Normal Levels of Consumption Do Not Effect Adversely Components of the Metabolic Syndrome and Risk Factors for Cardiovascular Disease
To be fair, there are a lot of articles on PubMed that say things like, "HFCS linked to arthritis/bronchitis/CVD/etc." The reason I didn't link those was not because they didn't suit my narrative -- notice I did link a study that found that people who consumed HFCS and sucrose-sweetened beverages ate more food. No, the reason I didn't link them was because I didn't think they were good studies because they couldn't establish HFCS as the causative factor. Was it the fructose, or just sugar in general? Or was it obesity? Conditions associated with obesity? There were too many confounders for which the studies didn't control, and they need to be repeated with better controls before they can be taken seriously.
Shall I give more links? Or am I to "shut up now?"
This book claims that Whites evolved differently due to their cruel environment which produced a cruel and barbaric race. There might be some truth in this...
Iceman Inheritance : Prehistoric Sources of Western Man's Racism, Sexism and Aggression: Michael Bradley, John Henrik Clarke: 9781879831001: Amazon.com: Books:
http://www.amazon.com/gp/product/1879831007
I will have a look to that book.
I used to look Lehninger Principles of Biochemistry, what do you think about this book?
Thank you.
life everywhere
rare earth
origins of life
a brief introduction
also some taped talks scroll down and click blue "seminar" links.
Oh right. I slightly misunderstood what you were looking for.
This may or may not be helpful but here's another recommendation:
https://www.amazon.com/Biological-Sequence-Analysis-Probabilistic-Proteins/dp/0521629713
While this book is pretty old and does not cover newer technologies and algorithms, I found it extremely helpful in understanding biological principles related to genetics and molecular evolution.
In this genomics era, we know so much more than just genetics now of course. But I mostly learned about genomics by reading tons of review papers, not a textbook. Once you study a bit on basic biology, I think reading review papers is the way to go if you want to delve into a more specific topic.
>Hey folks - if I understand the science correctly, it seems like the body can produce glucose from either protein or fat, is that right?
No, protein can undergo gluconeogenesis but fat cannot, fat is converted to ketone acids for use as energy. Amino acids are transformed in the liver into glucose via gluconeogenesis. These are primarily derived from digestion of protein you take in, and while your body can synthesize certain amino acids, it cannot synthesize histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, or valine, so the only way to obtain these are from dietary sources.
This chart on wikipedia explains the reactions needed:
https://upload.wikimedia.org/wikipedia/commons/1/16/Amino_acid_catabolism_revised.png
Wikipedia also does a decent job explaining why in humans you really can't have meaningful gluconeogenesis from fat, even if they've occasionally found a weird carbon atom or two in some experiments. https://en.wikipedia.org/wiki/Gluconeogenesis
Practically speaking, if you're not taking in any carbohydrates at all then all the glucose in your body is being derived from protein. You still need to eat sufficient protein on a ketogenic diet though, because your body really does have to have a minimum amount of glucose as some tissues (especially your brain) require glucose to continue functioning. So if you ate no protein at all your body would just start breaking down muscle tissue to fuel gluconeogenesis to keep your brain alive. In a sense you WANT there to be gluconeogenesis while eating a keto diet, just not too much gluconeogenesis that you're actually preventing ketone acids derived from fat from being the primary fuel source for yourself.
If you want to learn more about metabolism a couple books that are actually very thorough with the basics but are affordable are the BRS Biochemistry review book or Lippincott's Illustrated Review Series Biochemistry. Studying either one would give you a pretty good grasp of human related biochemistry. You can get older editions for just a few bucks used, not too much has changed in biochemistry over the last decade lol.
Lippencott's Q and A was useful for me. You can normally find pdfs pretty easily.
Also, Lippencott's Illustrated Review of Biochemistry was decent for summaries and a few practice questions at the end of each chapter.
>I was making the case which you can read in the studies above that OspA in desseminated infection can induce immunosupression through indirect mechanisms.
Which as I pointed out a very long time ago is pretty meaningless since OspA is expressed in the tick stage.
>Question, can not TLR2 agonists supress immune system?
No.
>Can not OspA interfere with the response of lymphocytes to proliferative stimuli including a blocking of cell cycle phase progression?
According to a single paper that was never cited and only used purified lymphocytes, maybe. But the immune system works together. Without T cells and macrophages together that's not very useful information.
>Yeah, I'm interested! What books do you recommend?
Janeway's [Immunobiology] (https://www.amazon.com/Janeways-Immunobiology-Immune-System-Janeway/dp/0815342438/ref=sr_1_1?ie=UTF8&qid=1505745700&sr=8-1&keywords=immunobiology+janeway+8th+edition) has been the gold standard for years. David White's [The Physiology and Biochemistry of Prokaryotes ] (https://www.amazon.com/Physiology-Biochemistry-Prokaryotes-David-White/dp/019539304X) and [Molecular Genetics of Bacteria] (https://www.amazon.com/Molecular-Genetics-Bacteria-Larry-Snyder/dp/1555816274/ref=sr_1_1?s=books&ie=UTF8&qid=1505745797&sr=1-1&keywords=molecular+genetics+of+bacteria) are the best microbiology references. For something more specific, ASM Press periodically puts out books on specific groups of bacteria.
I'm a second-year grad student in genetics/genomics, and these are the resources I go to for those oh-crap-I've-never-had-that-class moments:
This may be more than you want to spend (~$70), but Lynch has a really good book that details many of genomic elements and how they may have evolved. He assumes the reader generally understands transcription/translation, but the book isn't too technical.
If you have access from a company or university, Nature Reviews Genetics has reviews aimed at general scientific audiences for just about anything genetics/genomics related.
And, honestly, most Wikipedia pages for these kinds of topics have pretty reliable information as a first pass.
>I read The Cosmic Serpent, by Jeremy Narby (https://amzn.to/2J2IklU) and found it interesting. It's far from obvious what people can and can't see under the influence of psychedelics. And I didn't "claim" anything. I put forward a tentative hypothesis. That is by no means a claim. If you have a better idea, put it forward.
I once asserted the central thesis of a book I read. Now that I have been criticized for its ridiculous conclusion I no longer assert that. But just think about it, it is possible, you never know.
>I also liked this, for a slightly different take (on the universality of serpent/dragon symbolism): An Instinct for Dragons, by David E Jones: https://amzn.to/2IKnc0w
This is a book about the origins of the concept of dragons. Scientists might scoff but I see deeper than they do.
>Serpent imagery is unimaginably deep. For a discussion of the relationship between human beings and predatory reptiles (snakes, mostly) you could also read Lynn Isbell's fascinating The Fruit, the Tree and the Serpent: Why We See so Well: https://amzn.to/2IKJCTh
Snakes are dangerous, this is interesting.
If you aced ochem 343 and 345 biochem will be a breeze. It might be a good idea to take 507/508 though, as it is taught by the guys who literally wrote the book on the subject
I don't work in genomics specically but we do a lot of next generation sequencing. I am a biologist with interests in machine learning so let me try to summarize where people in biology use it:
Microarrays: Cancer research in particular uses this, but basically every biology discipline has some applications of this. Basically what you get is thousand of signal intensities, each represeinting expression of a gene, per sample, and what you are interested in is finding genes that behave differently from sample to sample. This is an example of a high-dimensionality problem, where the number of features is much larger than the number of samples. If you want some idea of how much work has been done in this area take a look at this (list)[http://www.geneontology.org/GO.tools.microarray.shtml]. You can more or less find all kinds of statistical methods here. As a biologist i should probably mention that i believe micro-arrays have problems with reproducibility that no amount of data-analysis will solve.
Gene prediction: This is a typical genomics problem in which we are given a long DNA sequence and told to identify the genes in it. Genes have some telltale signs, but these can be located with slight differences to each other and might be completely absent. Also, genes in eukaryotes are interrupted by socalled introns that do not code for genes (this story is a lot longer in reality). Poisson statistics on dna words (k long subsequences of dna) is the classical way of finding overrepresented dna features. Newer techniques uses HMMs and conditional random fields, as machine learning oriented as it gets. (This)[http://www.amazon.com/Biological-Sequence-Analysis-Probabilistic-Proteins/dp/0521629713] is a modern classic in all things sequence related.
Phylogeny: This is another of bioinformatics major contributions to modern science. Given some model of how evolution changes the composition of a sequence, we are interested in figuring out how organisms/proteins/genes can be related and building trees that can show us these relation.
Next generation sequencing: We can now generate much more data than we can process, we need some way of filtering as the machines can be inaccurate. We also need methods to cluster sequences within specific thresholds.
Sequence searching: This is a major topic. The most cited paper in the history of science is the one that announced BLAST. Machine learning is not as used here yet, but it probably will be if something faster than the traditional alignment algorithms come up.
This was just a short and incomplete overview, if you have specific questions i would be happy to answer.
If you want to browse widely used genomic/bioinformatic resources then look at NCBI, Ensembl, and UCSC.
If you want to try some bioinformatics problems, then see Rosalind.
If you want to learn biology, then buy textbooks on genetics/molecular biology. There are many, I recommend [this] (https://www.amazon.com/Human-Evolutionary-Genetics-Origins-Peoples/dp/0815341857) for human evolution.
If you want to learn about methods and sequence analysis, then [Biological Sequence Analysis] (https://www.amazon.com/Biological-Sequence-Analysis-Probabilistic-Proteins/dp/0521629713) is excellent.
If you want to explore widely used bioinformatics tools, then start with BLAST if you don't know it already.
This book was a life-saver when I was in grad school doing total synthesis
http://www.amazon.com/Advanced-Practical-Organic-Chemistry-Edition/dp/1439860971
As far as abiogenesis is concerned, I really enjoyed books such as The Emergence Of Everything, Beginnings Of Cellular Life, Origins Of Life, Genesis, What Is Life?, and Microcosms.
I'm an avid reader of all things abiogenesis, if you hadn't noticed. Considering it and finding ways to simulate it on a computer is one of my hobbies.
Also, Abiogenesis is really part of a larger study of emergence, chaos and order, and how simple things come together to perform complex dances. So on that note, I have a few more books worth reading:
Sync: How Order Emerges From Chaos In the Universe, Nature, and Daily Life, Emergence: From Chaos to Order, and Creation: Life and How to Make it
Them, plus Janeway's Immunobiology, Carey and Sundberg's Advanced Organic Chemistry part A and part B, Anslyn's PhysOrg, Ptashne's A Genetic Switch, Gilbert's Developmental Biology, Fersht's Structure and Mechanism in Protein Science and the NEB Catalog form a reference shelf for Biochem/Chemical Biology that I don't suspect will need updating for another decade or two.
EDIT: Except, of course, for switching out the NEB catalog every year for the new edition.
The best textbook I've had during my three years as a biochem/molecular bio major was Lehninger Principles of Biochemistry, hands down. Molecular Biology of the Cell was also decent, but not as clearly laid out in my opinion.
You're already on the right track getting started with Python, it is the most popular language currently. I would also highly recommend getting experience working in a linux environment, so either macOS or Linux, and getting comfortable working through the terminal. To round off your computational skills, I think that R would be a very good second language to learn. I'm currently using R more than Python for my work, it's much better to use when performing statistical analysis.
You should also try and get a good understanding of the biology behind the data you'll be working with. I think that THIS BOOK does a very good job at covering most concepts you're like to encounter in the field. It's what much of the biology portion of my graduate program was based upon.
Campell Biology is generally the number one go to for intro bio. My AP class, and intro class in college used it.
https://www.amazon.com/Campbell-Biology-10th-Jane-Reece/dp/0321775651
For more molecular stuff, molecular biology of the cell is fairly popular:
https://www.amazon.com/Molecular-Biology-Cell-Bruce-Alberts/dp/0815344325/ref=pd_lpo_sbs_14_t_0?_encoding=UTF8&psc=1&refRID=D9ZRY4BKB4ECZ2PMQRRJ
Anyone here read The Cosmic Serpent? Documented strangeness which validates what people here are saying.
I've randonauted a few times and found it worthwhile as a way to uncover some insights into my psyche. Same for dreaming. Last night I dreamt I was the new owner of a pet store. Workers were showing me the ropes. They said I had to open the store at 6 a.m. so I could open the drapes. Then they showed me a bunch of other stuff like making dog prints of their poop. And something about a parrot wherein I was advised to wear gloves because they can bite. Lots to unpack here...
Good book on the subject from an anthropological point of view, The Cosmic Serpent. It gets a little out there at points, but quite honestly I had a similar experience to the author. http://www.amazon.com/Cosmic-Serpent-DNA-Origins-Knowledge/dp/0874779642
> Every single living organism at their base level requires 3 things to live, DNA, RNA and Proteins, all of which are co-dependant on one another for existence (DNA needs RNA & Proteins to feed it, RNA needs DNA & Proteins to form it and Proteins needs DNA to form RNA to create it) and if even for a split-second they would cease to exist, and they probability of them to randomly form at the EXACT same time is, at best, in the TRILLIONS
This is an ill informed understanding of the central dogma and conflating it with de novo origin of life. I have absolutely no idea what your point is here other than conflating a bunch of scientific words together. Please clarify with links to the primary literature.
This wikipedia article is equivalent to what you would read in a high school level biology text about the central dogma. Otherwise, I have absolutley no clue what your point is here.
https://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology
> And the 2 mains factors in Genetic Mutation are "Point Mutation" and "Gene Duplication"; these can certainly account for Micro-Evolution, the changes one would experience that are minor and can even be achieved in one's lifetime, however studies into Micro-Evolution have revealed that this can NOT progress into Macro-Evolution, the change from one species into another, because of TWO things;
> 1) There is no guarantee that the mutation would be passed on or even continue to develop
> &
> 2) If the mutation was the result of some sort of outside factor, then a soon as it is no longer in play, the mutation near 100% of the time everses, disappearing altogether in the span of a few generations.
Wrong. This book here is a good primer on genome/gene evolution.
https://www.amazon.com/Origins-Genome-Architecture-Michael-Lynch/dp/0878934847
Please read it, and its references to the primary literature. Note that this text is just a primer. However, You are 100% wrong in your understanding of gene/genome evolution. It isn't my job to educate you, please read this book educate yourself and come back when you know something.
> Also even if that wasn't the case and a new species was born, unless they had a sibling of the opposite gender then if would die out with them because the DEFINING trait of a species is that it can't reproduce with another species, that's why even though dog come in a large variety they're STILL the same species, because they can have kids with one another, meanwhile Chimps and Humans can't, thus different species.
Wrong again. You do not appear to understand what a species concept is. Queller discusses this in detail and in terms of sociality.
A good place to start, but this is not all inclusive of species concept discussion.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2781869/
> Also unless they we're born with mutation, a female could NEVER pass it on, because their reproductive cells are never replaced as they age, also if the half of a parents genetic code doesn't posses the mutation their child WON'T inherit it. with this it is also argued that the mere existence of TWO genders disproves Evolution, because the chances of a mutation that gives birth to creature that needs another to reproduce happening and another mutation happening around the same time that needs to mate with the first creature to reproduce is ASTRONOMICALLY HIGH.
Wrong again. You are applying population genetics to the individual. This is grossly misinformed.
This is a quick primer
https://en.wikipedia.org/wiki/Population_genetics
Again, this is a very pedestrian article since it is wikipedia.
Until you have read https://www.amazon.com/Principles-Population-Genetics-Daniel-Hartl/dp/0878933085 you really should refrain from any discussion of population genetics, not to mention the volumous works of others this cites and have been built on these model.
> If you want visible proof then just look at humans and dogs, humans are everywhere on Earth, in various different environments and have had significant time for mutations to occur, however the biggest change was in skin colour and NO NEW SPECIES EMERGED, we're all still human. And with dogs, humans forced mutations to occur in them for over 100 years, thus if anything was going to scientifically replicate Marco-Evolution it was that, however instead of new species being born, the most we got was Inbred Monstrosities suffering from complete Genetic Failure AND THEY WERE ALL STILL DOGS
Again, you do not understand population genetics. This is completely wrong. As long as populuations are mixing, speciation is not possible. Again, see the Hartl book amongst many others. Heck, even Campbell's biology addresses exactly this point (a high school/freshmen biology text).
> Plus there's also the existence of Sequential Hermaphrodites, species with the ability to change gender, there is no scientific explanation for how they got this ability. And if you ask yourself HOW did they evolve that ability, an ability to rearrange their entire biology: Over millions of years? Since that ability is generally used to compensate for a missing gender, the species would die out long before that happened. And if you can't say a giant leap over at most a few generations or else you as well expect someone to just give birth to a baby that can shoo laser beams out of it's eyes.
Ok, so now we are talking about sex evolution? Obviously you haven't read this article, amongst many others it cites and have cited it.
http://linkinghub.elsevier.com/retrieve/pii/S0960982206016198?via=sd
Again, you are both wrong and do not understand.
> And there's also Crocodiles to consider, they've been around for 200 million years, longer than the dinosaurs, survived multiple Mass Extinction Events, and the only change they've gone through is becoming smaller, or the Coelacanth an ancient species of fish that first appeared 400 million years ago and was though to be extinct yet was discovered to be alive and unchanged from 400 million yrs ago. And you can't just say it's because they didn't need to because something any Evolutionist will point out is: "Evolution. IS. CONSTANT." If macro-evolution was real then regardless of whether they needed to or not, they would of evolved into new species. If it didn't work that way then we would still have Dinosaurs around unchanged from 75 million years ago, at least the aquatic ones anyway. The reason I used dinosaurs as my example is because they are extremely similar to crocodiles, thus if they nature of the planet changed so they couldn't survive, then neither could crocodiles.
Ok, here you have really exposed the fact that you do not understand population genetics. You really need to read biology by Campbell. Again, a highschool/freshmen level biology textbook. This is factually incorrect.
Crocodiles found their niche and survived. Dinosaurs did actually survive - they are modern day birds. Shockingly, they look different now because they evolved into new species. So it would seem that your best example (dinosaurs) is also factually incorrect.
Here is a recent paper among thousands http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001854 that says you are factually wrong.
> Also Evolution wasn't popularised by the Scientific Community, but by Atheists who keep pushing it to be taught in schools and push and teaching of religion out, such as the British Humanist Association an atheist group trying to get school kids to learn evolution with stories about dying due to not been good enough when change comes.
Again, factually incorrect. Darwin himself was religious.
https://en.wikipedia.org/wiki/Charles_Darwin
Pope Francis must also be an atheist.
https://www.usnews.com/news/articles/2014/10/28/pope-francis-comments-on-evolution-and-the-catholic-church
> Also forget not that just because a lot of scientists say something is fact doesn't mean it's true, cause over 100 years ago scientists said that going 40 mph would cause ones lungs to collapse and it has been repeatedly revealed that some scientists will lie for the sake of money or reputation and can even make outrageous claims due to perusing a crazy obsession. Evolution could very well be a "Cash Cow" for the Scientific Community because they don't tell us how much funding they receive for each field of research, the closest we got was when in 2011 the magazine Scientific American revealed that the over half of its funds go to a vaguely named field "LIFE" and even if we assume that 75% of that goes to medicine that would still make Evolution the 3rd highest funded Field of Research for scientists.
What? See above, now you are just getting looney.
I don't know of many scientists that are "getting rich" off science, especially evolutionary biologists. Please cite examples of evolutionary biologists as a population getting rich. I would like to know the mean and standard deviation of how rich evolutionary biologists are as a population. If you cannot produce this number, please retract this statement.
It actually comes from a book called The Cosmic Serpent
https://www.amazon.com/Cosmic-Serpent-DNA-Origins-Knowledge/dp/0874779642
I recommend this: http://www.amazon.com/gp/aw/d/1555816274/ref=mp_s_a_1_1?qid=1377491806&sr=8-1&pi=AC_SX110_SY165
Its a graduate level textbook. You should be able to find the 3rd edition used. It won't change quite as drastically as immunology does over a few years. For more specific information go to pubmed.
Read this and get back to me.
Here's some resources to get you started:
Saw The Manga Guide to Biochemistry on this sub a while ago, maybe it will help!
The Epigenetics Revolution looks suuuper interesting, and since I'm going back to finish my undergrad in genetics soon it would be nice to read some (mildly) relevant but still interesting stuff! for science!
The Encyclopedia of Early Earth looks like it has some interesting art in it. for art!
Thanks for the contests!
There's actually a good book on Ayahuasca, by an anthropologist named Jeremy Narby, called The Cosmic Serpent. I read it a few years back, and it's pretty entertaining, as well as informative.
I wanted to listen to part 2 before commenting.
I always love these dialogues. My particular fixation is with the collection of data, so this feeds my particular flavor of existence quite well.
As for content, this was my introduction to the term "pansychism" - even if I've previously been aware of the idea. So, thanks for that. I'm curious if you've read "The Cosmic Serpent" (https://www.amazon.com/Cosmic-Serpent-DNA-Origins-Knowledge/dp/0874779642)? It's an interesting panpsychic exploration of DNA instigated by an anthropologist's shamanic/psychedelic experience. Worth a read.
I'm also still digesting "neo-nihilism". Interesting idea, initially. Your conversation with Peter is a great example of why I've completely fallen in love with "psychedelic philosophy". Nothing is off limits, everything should be explored.
Thank you for bringing more of the exploratory spirit to us. Looking forward to more from you.
Edit: I LOVE your logo as well! Such a clean way to bring the yin/yang, forbidden fruit, and ouroboros out.
For a general overview of the history of traditional herbal medicine in the West, I recommend Barbara Griggs' book, Green Pharmacy: The History and Evolution of Western Herbal Medicine.
For traditional shamanic, magical use of herbal medicinal plants, I suggest you look into the Native American tradition(s). If you are looking for something in the area of psychedelics, I can recommend one book I liked: Cosmic Serpent: DNA and the Origins of Knowledge
For a bend towards energy medicine and the inner practice of herbalism, see Matthew Wood's books, for example The Practice of Traditional Western Herbalism: Basic Doctrine, Energetics, and Classification.
You can try this one:
https://www.amazon.com/Biological-Sequence-Analysis-Probabilistic-Proteins/dp/0521629713
It introduces one of the key problems in bioinformatics and should be fairly readable for someone of your background. It primarily adresses your first bullet, and does not go into many details about implementations,
Courses:
Take population genetics and computational biology. Population genetics focuses on dynamics of allele frequencies in different populations. Computational biology is anything from simulating networks of biochemical reactions to identifying patterns in DNA using hidden markov models.
Books:
http://www.amazon.com/Introduction-Systems-Biology-Mathematical-Computational/dp/1584886420/ref=sr_1_1?ie=UTF8&qid=1299531700&sr=8-1
http://www.amazon.com/Biological-Sequence-Analysis-Probabilistic-Proteins/dp/0521629713/ref=sr_1_1?s=books&ie=UTF8&qid=1299531747&sr=1-1
> Lets look at the source on the website. "From Lehningher principles of Biochemistry..." Originally published: 1970. So a source 47 years old. That makes sense, no chance science has advanced one iota in half a fucking century.
The seventh addition was published in 2017. What made you think I was referencing the 1970 edition? Oh, you're a biased Darwinist.
https://www.amazon.com/Lehninger-Principles-Biochemistry-David-Nelson/dp/1464126119
Read it an weep.
>Haloferax volcanii, a Prokaryotic Species that Does Not Use the Shine Dalgarno Mechanism for Translation Initiation at 5′-UTRs Published: April 14, 2014
>A translational enhancer derived from tobacco mosaic virus is functionally equivalent to a Shine-Dalgarno sequence. Proc Natl Acad Sci U S A. 1989 Jan; 86(1): 129–132.
Yes, more gaps and transitions to fill. You really don't get it do you. But at least you're making a good attempt at at a response which is more than I can say for this guy:
https://www.reddit.com/r/THUNDERDOME_DEBATE/comments/6auvhc/does_the_professor_of_darcrapolgy_think_selective/
You even listen to Terrence McKenna?? Lol you'll be fine! I say go for it.
The thing about Terrence McKenna is that, like his brother Dennis said,if he's right about even 1% of his claims, that's a very important thing in the world.
I read a book once on ayahausca and DNA where this geneticist did an anthropology thing where he went and did ayahuasca with tribes in South America to scientifically prove a connection between ayahausca and DNA. It's a VERY interesting read. He does a great job at dumbing it down to laymen's terms so that someone who's not a scientist can read the book and understand it. Then the second half of the book is all works cited. Sources for every single claim he makes during the book. So if someone wanted to they could see proof for all the things he was claiming. He does great at not adding any of his personal beliefs into the book as well, it is purely scientific. It's called the cosmic serpent : Cosmic Serpent: DNA and the Origins of Knowledge https://www.amazon.com/dp/0874779642/ref=cm_sw_r_cp_apa_5QgMBbG18AQY8
A book that you may be interested in is called 'The Cosmic Serpent: DNA and the Origins of Knowledge.' It's a really good read and not too long. https://www.amazon.com/Cosmic-Serpent-DNA-Origins-Knowledge/dp/0874779642
For the basics, I still think this is one of the best.
https://www.amazon.com/Biological-Sequence-Analysis-Probabilistic-Proteins/dp/0521629713
> biologically pre-disposed (for lack of a better phrase) to be good candidates for therapies like cbt and dbt?
Basically, yes. It appears the majority of people it is very helpful. However, some people do not respond at all. There (currently) appears to be no rhyme or reason behind that. But we (more or less) know there is no physiological reason (fMRI or something can't tell us someone wont respond).
>Could you suggest an introductory text for someone with a basic understanding of the brain?
Honestly, not really. I don't pick the textbooks the undergrads/1st years read :P Lehninger Principles of Biochemistry is good for getting a firm footing for the biochemical pathways and such.
Basic Clinical Neuroscience is a good foundation textbook, but I can't remember how much biochem you need to understand it. Molecular Biology of the Cell is another good intro text to molecular biology, if that's what you're in to.
I've been a research assistant, not a teaching assistant for the past decade (oh my god, I'm old lol).
edit: Also if you didn't see it before, see also the edit in my previous post.
You're also the person that thinks fat is a carb and that zero sugar kills. Give me a break. Do your reading. Here's some more. You're welcome.
http://en.wikipedia.org/wiki/Essential_nutrient#Carbohydrates
http://highsteaks.com/forum/health-nutrition-and-science/nutritional-ketosis-vs-ketoacidosis-369.0.html
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2129159/
http://www.nal.usda.gov/fnic/DRI//DRI_Energy/265-338.pdf
http://www.amazon.com/Biochemistry-Lippincotts-Illustrated-Reviews-Series/dp/1451175620
http://www.amazon.com/Marks-Medical-Biochemistry-Lieberman-Markss/dp/160831572X
http://books.google.com.au/books/about/Essentials_of_Human_Nutrition.html?id=KPaEAAAACAAJ
http://books.google.com.au/books?id=hRoRff4PH6wC
http://books.google.com.au/books?id=bSvyL2JCsLwC
It's an archetype in the human brain. I've seen snakes on different psychedelic substances, most notably ayahuasca.
Jeremy Narby wrote a very interesting book about snake symbolism, psychedelics and DNA called 'The Cosmic Serpect'. Highly recommended.
http://www.amazon.com/The-Cosmic-Serpent-Origins-Knowledge/dp/0874779642
I'd recommend reading the Cosmic Serpent ( http://www.amazon.com/The-Cosmic-Serpent-Origins-Knowledge/dp/0874779642). Narby seems to think that psychedelics allowed native people to have direct access to DNA and that it is represented in art as two intertwined serpents. Very entertaining and interesting.
Everyone should read the Cosmic Serpent. It's a little boring in the middle but don't give up halfway through. Definitely an amazing book.
You should start reading The Cosmic Serpent: DNA and the Origins of Knowledge if you haven't already. It's sitting in my "to read" pile, but if my journey took me in the direction that your experience seems to suggest, I can guarantee I'd be fast-tracking it to the top of the pile.
If you're unfamiliar with Jeremy Narby, check out this interview over at Deoxy. I have a feeling some of his notions might compliment your own.
Thanks! :) That's a really good idea to wait until you are ready as mindset and intention matter quite a bit.
General Information:
/r/Ayahuasca
-http://forums.ayahuasca.com/
-good forum with general knowledge
-https://www.dmt-nexus.me/forum/
while it's mostly dmt centered, this is probably the best entheogen community online. Has some good writeups on Ayahuasca and DMT visuals are often pretty similar to Ayahuasca since it's the same chemical in most brews(n,n dmt). Breakthrough visuals are much more common on DMT but healing is rarer in my experience.
https://ayaadvisors.org/
Great review site for retreat centers. There are more in the US, especially if you look around.
Books:
The Cosmic Serpent
The Ayahuasca Test Pilot's Handbook
As for posts, this one from dmt nexus is a good primer:
https://www.dmt-nexus.me/forum/default.aspx?g=posts&t=8972
Hopefully that's enough to at least get the ball rolling. Feel free to reach out if you have any questions!
Google around, find websites for university degree programs in biology, biochemistry, genetics, etc., and mine the syllabi for textbooks that are used. That would probably give you a decent seed list.
Read popular books for lay-people on biohacking and related topics, like Biopunk, Frankenstein's Cat, Regenesis, Life at the Speed of Light, A Crack in Creation, etc., and then use Google / Wikipedia to drill down on the topics you find discussed there.
One other book that has been recommended to me by actual experts from our local biohacking group is Molecular Biology of the Cell
Also.. It's fully possible for humans to create a mix that stops aging in whatever age someone is in? In theory?
I don't think anybody knows the answer to that yet.
I like Voet & Voet for introductory general biochemistry.
Principles of Physical Biochemistry is a good selection for an introduction to biophysical chemistry. You will need a sound foundation in physical chemistry to make the most out of this book, though.
Alan Fersht's Structure and Mechanism in Protein Science is another good choice, especially if you want to firm up your understanding of the essentials of enzymology and protein folding.
I don't really want to comment on your postulates or discourage your thinking, but I would recommend the book, The Cosmic Serpent, in which an anthropologist examines shamanic traditions in the Amazon.
The question of how these shamans discovered the use of specific hundreds of assorted plants in the Amazon, out of the choice of tens of thousands, that cured, nourished, or tripped-out their people for millenia is central to the book, and doesn't require recourse to divine inspiration-- but it is perhaps as recondite and mysterious. It seems like a similar path of inquiry, and a wholly illuminating book of quality ethnobotany and anthropology.
Good luck in the search for truth... but it might not be wheat.
Maybe? This is something I've learned through experience, observation and meditation. But a lot of things will elaborate this principle. First thing that comes to mind is the four forces in physics, recently being understood as one single force that has settled into four discreet manifestations. Thats kinda hard to wrap your head around without a lot of physics knowledge though.
However, there is a book called The Cosmic Serpent that has at least one chapter that is illuminating on the subject. I've only read the bits on Google Books though.
The pretentious part of me wanted to say "only the book that is the universe," but thankfully good taste prevailed.
Halliday Physik German
Fundamentals of Physics Halliday US Version
That's kinda fucked up oO
Edit:
Biochemistry the same: Germany edition - US Edition
Freeman Dyson already did something similar in chapter three of this book. In particular, check out the Figure 4 on page 65.
http://www.amazon.com/gp/aw/d/1439860971
I'd recommend buying and reading this book as it covers most of the basic as well as slightly niche techniques you will need during your time in a synthetic lab. This is particularly useful for learning how to set up efficient columns (how polar a solvent system to use, and how much silica to use for a given mass of crude material).
Specifically regarding yields, TLC is a great tool, both to check if a reaction has gone to completion (limiting reagent starting material present will inhibit yields) but also when using a separating funnel (say you are extracting into an organic solvent, you can TLC the organic layer after 4 extractions and if there is no product observed, then you know you won't have any material left in your aqueous layer).
It's always best to do reactions under nitrogen, and always make sure to use dry solvents (from a still or solvent purification system) when using moisture sensitive reagents e.g. NaH.
There are many other tips but they are reaction specific, but I will say the more time you spend in the lab, your yields will naturally increase as your skills improve (as long as the reaction allows it). Good luck!
Durbin's book, Biological Sequence Analysis is very good.
Some books on stochastic processes are useful.
Some HMM material
Also, a few journals that I read: Genetics, PLoS Biology/Genetics, MBE, GBE, and Theoretical Population Biology. If access is a problem, look to PLos, arxiv, bioRxiv.
I have a PDF of Lippincott but I may pick up the Q&A. Is it this book?
https://www.amazon.com/Lippincotts-Illustrated-Q-Review-Biochemistry/dp/1605473022/ref=sr_1_9?keywords=lippincott+q%26a&qid=1562948767&s=books&sr=1-9
Did you use any Anki?
Also this is awesome, thanks so much.
No, you missed my point I think.
The radiated heat is EXCESS heat, you drinking cold water will just cause the body to dispell less heat.
The body dont care about the amount of heat it radiates, there will be zero increase in metabolism.
The nerves in your stomach and digestive tracts dont contain thermoreceptors, so your body will never "shiver" to increase the metabolism thus increase the heat.
Even if you swallowed icecubes youd achieve nothing other than the damage the cold might do. If, however, you digested enough cold water so that the energy you radiate is less than the energy needed to warm the water, then yes, but at that point you would be shivering. Your body dont just "increase chemical reaction x", which metabolic function do you even suggest that would be?
Also, unless you are in a room at 0 degree celcius, you are failing to account for the energy recieved.
To make sure I hadnt forgotten any of the basics from the bachelor/masters degree, I doublechecked both
http://www.pearsonhighered.com/product?ISBN=0321750004
and
http://www.amazon.com/Lehninger-Principles-Biochemistry-David-Nelson/dp/071677108X
Our body have no "use energy cycle", developing something like that evolutionary would just not occur. And the "increase heat cycle", which is achieved through increased mechanical work, as response a decline in temperature, requires input from thermoreceptors, which you dont have in your gut.
I found The Epigenetics Revolution to be both informative yet accessible. Would strongly recommend.
That would KILL me! o_O I have ten-pound books! =[
The Epigenetics Revolution. A book about genetics and molecular bio, rather than biochemistry, but this is a pretty good book.
You don't exactly sound like a complete layman though, so I say there's nothing wrong with picking up a textbook like Stryer and seeing which topics interest you!
I recommend this book. I read it a while back and remember it having some good information on Ayahausca and its tribal uses. I'm pretty sure that the author also tries it and gives his report.
My one line advice: take an introductory molecular biology course or genetics course.
If you have a summer, do this:
Read "The 8th Day of Creation" if you want to learn the whole of molecular biology's roots in one book. It is written on the college-educated "lay" reader level and details the history vividly.
Then check out and admire some websites:
genome.ucsc.edu
wormbase.org
flybase.org
start messing around with it and get a feel for the scope of it. Others can add more.
Then, there are some textbooks. I know people who like this one
The Manga Guide to Biochemistry
the gold standard.
op: http://www.amazon.com/Biochemistry-Lippincott-Illustrated-Reviews-Series/dp/1451175620/ref=zg_bs_13511_8
Inner Paths to Outer Space by Strassman and three others
http://www.amazon.com/Inner-Paths-Outer-Space-Psychedelics/dp/159477224X
The Cosmic Serpent by Jeremy Narby
http://www.amazon.com/Cosmic-Serpent-DNA-Origins-Knowledge/dp/0874779642/ref=sr_1_1?ie=UTF8&s=books&qid=1302588552&sr=1-1
Astrothelogy and Shamanism by Andrew Rutajit asd Jan Irvin
http://www.amazon.com/Astrotheology-Shamanism-Christianitys-Revolutionary-Reinterpretation/dp/1439222436/ref=sr_1_1?ie=UTF8&s=books&qid=1302588605&sr=1-1
The Sacred Mushroom and the Cross by John Marco Allegro
http://www.amazon.com/Sacred-Mushroom-Cross-Christianity-fertility/dp/0982556276/ref=sr_1_3?ie=UTF8&s=books&qid=1302588605&sr=1-3
these guys have some good interviews and a movie called "The Pharmacratic Inquisition" for free on the site
http://www.gnosticmedia.com/
While I haven't read this one, it purports to answer some of these questions
https://www.amazon.com/Cosmic-Serpent-DNA-Origins-Knowledge/dp/0874779642
(it does seem far fetched, although listening to the video in the OP, I'm having trouble finding where JP mentioned DNA specifically... Can anyone please link hr:mn:sc?)
If you want actual science behind it I highly recommend reading an actual book students are taught from: Leninnger Principles of Biochemistry by) (this are clean, non-affiliate links). You should be able to borrow it from the library, any edition should do.
Specifically the chapter on human metabolism, and pay attention to what is a set-point.
This is all not new, it has been known for ages. Dr Fungs books started popularizing this knowledge recently, thumbs up to him for that
http://www.amazon.com/Biochemistry-Lippincott-Illustrated-Reviews-Ferrier/dp/1451175620/ref=sr_1_3?ie=UTF8&qid=1459285446&sr=8-3&keywords=biochemistry
Voet and Voet. I swear by this book. It's damn near encyclopedic.
No asking questions! You need to read this and this.
Biology is nothing without chemistry so you need to know the basics of chemistry as well. My favourite book is the Color Atlas of Biochemistry by Jan Koolman, K. Rohm.
Another very useful book is Biochemistry (Lippincott Illustrated Reviews Series) by R. Harvey.
Many past participants recommend the Lehninger Principles of Biochemistry, however, this book may be too detailed for olympiads.
GENETICS TEXTBOOKS|
Genetics: Analysis and Principles (WCB Cell & Molecular Biology) by Brooker presents an experimental approach to understanding genetics and what I like most is that there are plenty of problems with explanations and answers. Another good textbook for genetics is Genetics: From Genes to Genomes, 5th edition by Hartwell. Genetics: From Genes to Genomes is a cutting-edge, introductory genetics text authored by an unparalleled author team, including Nobel Prize winner, Leland Hartwell.
GENERAL BIOLOGY TEXTBOOKS|
It is not a secret that the Bible of Biology is Campbell Biology (11th Edition). It is a good book and it covers all fundamental biology topics, nevertheless, some topics are discussed only concisely so some good books in addition to Campbell’s could come in handy.
HUMAN ANATOMY |TEXTBOOKS
For human body anatomy and physiology great books are Human Physiology: An Integrated Approach (7th Edition) by Dee Unglaub Silverthorn or Vander’s Human Physiology.
MOLECULAR AND CELL BIOLOGY|TEXTBOOKS
My top choice for molecular biology is Molecular Biology of the Cell by Bruce Alberts, et al. This is book is a big one, a hard one, an interesting one, a useful one. From my point of view, current and upcoming IBOs are focusing on molecular and cell biology because these fields are developing so rapidly and thus these branches of biology are perfect source for olympiad problems. So try to read it and understand it. If you want something cheaper than Alberts but equally useful, try Molecular Biology of the Cell, Fifth Edition: The Problems Book
PLANT BIOLOGY|TEXTBOOKS
Many past biology olympiad questions contain quite a lot of problems about plant anatomy and physiology. Thus, I suggest to read Stern’s Introductory Plant Biology. Another amazing book for plant biology is Biology of Plants by Peter H. Raven, Ray F. Evert, Susan E. Eichhorn.
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TEXTBOOKS FOR AND PROBLEM SOLVING|TECHNIQUES
Science competitions test a student’s level of knowledge, power of scientific reasoning, and analytical thinking outside of the regular school curriculum. A systematic approach and smart study regimen are both required to get good results in science competitions. This is where my book How To Prepare for the Biology Olympiad And Science Competitions by Martyna Petrulyte comes into the picture.
We can digest cellulose?! I've never researched the topic so I've got no idea. I've been under the impression that any digestion of "fiber" (such a vague term! I have a feeling it'll be going out of style in the coming decades) was through gut bacteria, but again, I've never really done any research on it. Good call on whether hydroxyproline/hydroxylysine can be utilized by gut bacteria. It wouldn't surprise me at all if they could.
Digestion isn't my forte either beyond knowing where things get broken down/absorbed. I've been meaning to hit up gut bacteria since they're becoming so popular topic these days.
Lotta respect for you too dude! And everyone here who contributes discussion. The more we talk things out and try to see where we might be overassuming/flat out wrong/missing information, the more we learn. That's the beauty of the scientific method, in my opinion. I've got high hopes for this sub.
Not sure if FFA/glucose radicals are handled by different antioxidants. That would definitely make sense, though, considering the unique antioxidant utilities of vitamins C and E each.
I have no idea if any nutrients are more bioavailable from plants than animals. Some would be exclusive (or nearly so) to one category, like taurine in animal products or beta-carotene in vegetable products. There are a lot of factors to consider in food bioavailability too, like cooking methods, usage of oils, cooking time, all that stuff.
> Perhaps physiological insulin resistance? And perhaps something like this hints that physiological insulin resistance isn't a good thing; you've reached a point of ketosis that is too "deep" and are pushing starvation. (Subtly referring back to the body's need to replenish aminos from diet).
I was wondering about that. I've yet to examine Mr. Dobromylskyj's hypothesis of physiological insulin resistance in depth.
> That would mean a lot for an all meat diet since it's argued that vitamin E is one of the nutrients that would be deficient.
Isn't that one of the better arguments against it? ;) I figure, hunter-gatherer societies have eaten varying proportions of foods derived from animals and plants, it's possible, even probable we would be okay going proportionately in either direction. Though, I'm more a fan of moderation... :)
I think my secret is a huge interest, which keeps me going in researching/learning about biochemistry. Even still I learn new things all the time, and ideas I previously had turn out to be wrong.. c'est la vie. I can't imagine taking up, say, mechanical engineering, I just don't have much an interest in it. Hopefully you get to take some kind of chemistry class! (Idk, most biochem classes I know of around here are higher-level/require several prerequisites). Really cool that you play the guitar btw. Piano player here.
Learning new/challenging material sure isn't easy but it's very rewarding. I started learning some basic cell biology by just looking at wiki pages and exhaustingly detailing every last definition that I didn't know like the back of my hand. It all expanded from there and I started doing the same with primary literature (what I often read here; bscly all research that's not a review). If you're looking for a textbook, I highly recommend Lehninger et al's Principles of Biochemistry. ^^^Pop ^^^me ^^^a ^^^pm ^^^if ^^^you ^^^want ^^^a ^^^PDF ^^^of ^^^the ^^^book
It depends on which subject you are practicing for. I'll just link biochemistry book but just change biochemistry to any other subject name and it will show up.
https://www.amazon.com/Lippincotts-Illustrated-Q-Review-Biochemistry/dp/1605473022/ref=sr_1_1?s=books&ie=UTF8&qid=1549012238&sr=1-1&keywords=lippincott+q%26a+biochemistry
Ernst Mayer, Jerry Coyne and Richard Dawkins have written some decent books broadly covering the evidence for evolution. Donald Prothero's Evolution: What the Fossils Say and Why It Matters fits into that general category, and does a good job of outlining the evidence for evolution as well, in particular from a paleontological perspective.
Astrobiologist / Paleontologist Peter Ward has written a ton of fantastic books. I'd start with Rare Earth, which outlines the Rare Earth hypothesis, ie complex life is likely rare in the universe. If you read Rare Earth, you'll come away with a better understanding of the abiotic factors which influence the evolution of life on Earth. If you end up enjoying Rare Earth, I'd highly recommend Ward's other books.
Terra, by paleontologist Michael Novacek describes the evolution of the modern biosphere, in particular from the Cretaceous onwards, and then discusses environmental change on a geological scale to modern environmental challenges facing humanity. It's one of those books which will change the way you think about the modern biosphere, and the evolution in the context ecosystems, as opposed to individual species.
Another book by a paleontologist is When Life Nearly Died: The Greatest Mass Extinction of All Time, looking at the Permian mass extinction, which was the most catastrophic mass extinction of the Phanerozoic wiping out 95%+ of all species. More focused on the geology than the other books I mentioned, so if you're not into geology you probably wont enjoy it so much.
Biochemist Nick Lane has written some great books. Life ascending would be a good one to start off with. Power, Sex, Suicide: Mitochondria and the Meaning of Life is really excellent as well.
The Origins of Life and the Universe is written by molecular biologist Paul Lurquin. It mostly focuses on the origin of life. It's pretty accessible for what it covers.
Another couple of books I would recommend to people looking for something more advanced are: Michael Lynch's Origins of Genome Architecture, which covers similar stuff to much of his research, although takes a much broader perspective. Genes in conflict is a pretty comprehensive treatment of selfish genetic elements. Fascinating read, although probably a bit heavy for most laypeople.
You're missing the point. Nobody is saying homosexuals are "really straight". Homosexuals like the same sex, there is no doubt about it. But science has found there is no biological basis for the origin of homosexual behavior. I recommend reading The Iceman Inheritance for details.
1st pass:
Get your hands on Brock or Prescott (standard microbio textbooks) and read the chapter on Archaea. These books are good if you want an overview of the group in general, but if you want something more specific, this isn't the book.
2nd pass:
Get your hands on Bergey's Manual of Systemic Bacteriology. My microbio professor who works on Archaea swore by this book. Depending on the edition, you will find notes on the various species and genera that are not only interesting but also help in their classification.
For general principles of protein folding and stability, I would recommend the following:
Nutrition is mostly about biochemistry. So I'd recommend you reading some biochemistry books instead of nutrition based ones. Once you have a solid knowledge of biochemistry you'll be able to understand nutrition without a problem.
I bought this last year just for fun
Your DNA. Seriously. Maybe.
Read this book: The Cosmic Serpent: DNA and the Origins of Knowledge by Jeremy Narby
https://www.amazon.com/Cosmic-Serpent-DNA-Origins-Knowledge/dp/0874779642
Biochemistry was absolutely terrible. That was the hardest I worked in undergrad and the happiest I ever was to receive a passing grade. We had a similar set up where there were three or four tests and that made up the entirety of the grade for the class. Just to reiterate what others have said: CASPA will average the two grades. No way around that. Don't let that get you down though. Do well when you retake the class and do well in your other science classes and it should be fine. I would definitely look at taking other high level biology classes to demonstrate you can do well in higher level academics. Biochemistry for Dummies was actually really helpful. https://www.amazon.com/Biochemistry-Dummies-John-T-Moore/dp/1118021746 Khan Academy was also really helpful. They don't have a biochemistry topic but they do have a section for MCAT prep which covers a lot of the topics presented in biochemistry. https://www.khanacademy.org/test-prep/mcat/biomolecules
I had to withdraw from A&P and had to retake a psych class. Nothing was mentioned about my grades during my interview for PA school. Best of luck to you.
For which one? CRISPR? Well you won't be able to understand the details until you have a good grasp of molecular biology. But molecular biology itself is a huge area. I would like to give you recommendations but it's really hard with your interests so broad.
It is like asking for book recommendations on Linear Algebra: there are tons and some focus on numerical methods, others on eigenvalues, others on decomposition methods like SVD, others on applications in machine learning, etc.
Maybe start with something like this:
https://www.amazon.ca/gp/product/0815344325/ref=pd_lpo_sbs_dp_ss_1/187-9306447-5023949?pf_rd_m=A3DWYIK6Y9EEQB&pf_rd_s=lpo-top-stripe&pf_rd_r=0A3FAK9C4CRAFZQTEQ4H&pf_rd_t=201&pf_rd_p=1977604502&pf_rd_i=0815341059
or this
https://www.amazon.com/Molecular-Biology-Robert-Weaver/dp/0073525324/ref=sr_1_2?ie=UTF8&qid=1479421339&sr=8-2&keywords=Molecular+Biology%3A+Robert+Weaver
for molecular biology.
For introductory genetics, pretty much any undergraduate level biology or biochemistry textbook will help you understand the basics of transcription, translation, genes, heredity, etc. Once you have a thorough understanding of what a gene is, what a regulatory region is, what epigenetics is, what types of mutations occur etc. then you'll have a good idea of which specific questions to ask to explore a certain topic in more detail.
I would also spend time on the wikipedia pages and other sources reading about the different sequencing methods that are central to genetics. Look up Sanger sequencing and explore some of the next-generation-sequencing (NGS) techniques now available. Fully understanding these will also require knowledge of biochemistry, such as phosphodiester bonds, and basic biology techniques and physics such as electrophoresis and fluorescence.
Understanding and diving into CRISPR, genetic engineering, synthetic biology, etc. will require a thorough understanding of the above, and then more detailed knowledge on gene expression, how it is manipulated, about things like plasmids, retroviruses and their molecular machinery, etc.
Then there are people who develop algorithms for bioinformatics that probably know little to none of the above and don't need to for their day to day work; the answer is in general "it depends".
I recommend also reading Jeremy Narby's book "The Cosmic Serpent: DNA and the Origins of Knowledge."
Let me recommend An Introduction to Systems Biology: Design Principles of Biological Circuits by Uri Alon. This book is extremely well-written and approaches cellular systems from the perspective of an engineer or physicist. It will help to orient you to the "big picture" of how cells work without swamping you in molecular details. Systems biology is a hot, emerging field at the intersection of molecular biology, biophysics, and computational biology. Feel free to PM me if you're interested in the field and want a few suggestions about which are the top labs.
I would recommend getting more information about the molecular details elsewhere. I haven't read Alberts, but it seems like a classic text (I often see it on bookshelves). I read Watson's Molecular Biology of the Gene, and thought it was quite good.
For a biochemical perspective, I recommend Stryer's Biochemistry, which covers many common biological molecules. It is a very readable classic and serves as a good reference text. It should give you an idea of how the molecular machines operate on a chemical level.
You can probably find these in your school's library.
Edit: Just realized this post is 3 months old (hah). Hope this helps nevertheless.
I kept them (the engineering ones at least). At great personal cost though.
Every now and then I hit one or two of the key upper level books specially within heat transfer, fluids, thermo, and process design. I even had to break out a math book once or twice. But, I work a design job where such references will pop up. If I was running a process or running a plant I doubt I would have had the need.
Also, your text books aren't worth NEARLY what you think they are... new editions pop up all the times, and even a year or two will render their value on the market to "pretty low" despite the content of course being super useful.
Anyways... I kept mine, and my wife made me build a large built in bookshelf to house them and then put me on a book in/book out diet because I have so many god damn books. I actually have two degrees (Biochemistry too) and I had all my biochem books. Even though I have ZERO need for them, getting rid of MOST of them was REALLY hard, despite the information not even being accurate anymore (degree was in 2003).
Now my Lehninger's Biochemistry book (https://www.amazon.com/Lehninger-Principles-Biochemistry-David-Nelson/dp/1464126119/) and Albert's The Cell (https://www.amazon.com/Molecular-Biology-Sixth-Bruce-Alberts/dp/0815344325/) are used as "rug flatteners" for our area rugs because they are so heavy.
She's a vet... and one of the first things she did was part with all her vet books except for a few.
And another
http://www.amazon.com/gp/product/1429234148/
Interestingly enough https://www.amazon.com/gp/aw/d/1259188124/ and https://www.amazon.com/gp/aw/d/1464126119/ref=mp_s_a_1_1?ie=UTF8&qid=1520567419&sr=8-1&pi=AC_SX236_SY340_FMwebp_QL65&keywords=lehninger+principles+of+biochemistry+7th+edition&dpPl=1&dpID=51S8Bgm9FmL&ref=plSrch disagree with your text. And, seeing as I have more experience with both these texts, and poisons and toxins fall into what I do professionally, we're going to have to agree to disagree.
The Cosmic Serpent: DNA and the Origins of Knowledge
A MUST read for anyone who has ever partaken :)
https://www.amazon.com/gp/aw/d/0815344325/ref=dp_ob_neva_mobile
Best book ever on the subject.
The Cosmic Serpent is a good book on the subject.
http://www.amazon.com/The-Cosmic-Serpent-Origins-Knowledge/dp/0874779642
Racism; as we know it today in the Western world, and especially U.S.A. ; is a construct with a very particular occidental origin. The origin is important to understand the answer to your question, and why you may change your view. I will not respond to the surface level that i expect many others already have. I will say what i KNOW has not been said, and something for you to think on for fun. There is a biological basis for racism in the psychology of the western man. This is based off the fact that the melenated genome is "preferred" or selected in the theoretical process of Evolution by Natural selection. If a black man has a child with a white woman, the child is black. If a white man has a child with a black woman. the child is.....black. 99% of the time. The black genome contains ALL potentialities ,and phenotype for every race that exist. Cecil Rhodes, Darwin, and others realized this as a major threat to the survival of the white race a long time ago. I name those individuals because there is very interesting history reflecting the codified "policies" that became a part of the foundation of White male conquest over African(and other melanated) human populations. Look up the statistics for white birth/death ratio. People evolved under the Sun, the sun has everything to do with the biological reality, that actually FUELS the long-lasting xenophobia that has been expressed in the western white male for centuries since the ending of the last ice age. Look into (The Iceman Inheritance, and The Cronus Complex).
How people behave when walking down the street is easy to break down , and understand. It is easy to rationalize. You will realize that such behavior is not racism at all. Racism is a survival based behavior that is born out of an imperative to reconcile and irreconcilable reality. That reality is: White Europeans are Homo Sapiens that suffered from a mal-adaptaion to the environment due to the extended survival period during the last ice age. Surviving above the 54 parallel about 20,000 years ago meant existing LITERALLY between fire and ice in an environment that never saw the full sunlight for 100s of years. The lack of sunlight caused the lack of melanin. Melanain is useful in places where the sun is intense, but it works against the fetal development in places where the sunlight spectrum is not as full. It is the same reason that Polar bears are white, although it 'appears' sunny at the north pole all the time. It is a spectrum of sunlight that lacks a crucial element that is needed by the human to develop in the way we developed in our earliest days in so-called Africa.
So.... RACISM steams from a violent response to the biological imperative.
I link to understanding the Skin Pigmentation science that i butchered:
https://www.ted.com/talks/nina_jablonski_breaks_the_illusion_of_skin_color
The Link to an explanation on the theory of maladaptation caused to some of the human family during the ice age.
https://www.youtube.com/watch?v=cFpBdpRIyMU
https://www.youtube.com/watch?v=erbbcR8kKjI
And Finally a great book on The Cronus Complex caused by lack of vitamin D via sunlight
https://www.amazon.com/Iceman-Inheritance-Prehistoric-Sources-Aggression/dp/1879831007