Archive for the ‘Bruce Lipton’ Category

h1

Bruce Lipton’s ‘Biology of Belief’ – Annotated with facts: Part 17 (Lipton is an extreme environmental determinist)

December 5, 2017

Before returning to the many hornets’ nests of errors that Lipton has placed throughout this book, it will be worth considering in isolation a couple of Lipton’s more foundational errors. Chapter Three is a complex of several extraordinarily complicated knots of factual errors, misrepresentations, and misunderstandings that it is impossible to unpack them in the sequence that they appear without going on long excursions up entirely pointless garden paths. So the next two or three posts will deal in isolation with a specific foundational problem.

This post will consider Lipton’s extreme version of environmental determinism. Lipton’s position here reflects many of the errors of the mid-20th century ideology that posited that humans are born as a blank slate, free of instincts and in-born propensities, to be “written upon” by their surroundings. More fanatical of theorists in this area, especially the Behaviorist school, saw the tabula rasa of childhood as an opportunity to inscribe upon the central nervous systems of the young, whatever they pleased. Marxist, communist and even some religious theorists and cults see the training of the young as the foundation stone of the ideal society. Disasters have generally followed.

Lipton, as we shall see as we go through this book, has decided that adults are capable of re-writing not only their own behavioral ‘programs’, but even reconstructing their own physiology to an extraordinary degree. This leads directly into his cancer quackery.

Lipton presents his case as a reaction to the supposed “genetic determinism” which he wrongly thinks is the norm for scientists, and — with breathtaking ignorance — equates with the’Central Dogma’ of genetics. (The jokingly named ‘Central Dogma’ holds that DNA is not altered by the proteins it creates. Genetic determinism is an ideology that deals with behavior.)

In order to fabricate a “debate” in science between the extremes of “fate” being written genetically in stone, and the supposedly blank slate of human nature, Lipton has resuscitated the old “nature vs. nurture” controversy of the 20th century. This highly polarized debate still draws people into accepting a position on a spectrum.

As neurobiologist and primatologist Robert Sapolsky has pointed out in his recent book Behave, advances in science, more abundant and more accurately collected data have, in recent decades rendered the distinction between nature and nurture largely irrelevant. However the debate has continued in the popular imagination. Unfortunately this debate promotes misunderstandings and precludes or prevents a correct understanding of genetics and development. Genetics is a weird subject, and requires a new way of conceptualizing biology. Neither the nature, nor the nurture pole has a corridor that leads to understanding it. Genetics itself, has transcended the debate, and made it irrelevant.

As Sapolsky has put it, even talking of genes and environment “interacting” is too polarizing. “The problem with “a gene-environment interaction” is the same as asking what height has to do with the area of a rectangle, and being told that in this particular case, there is a height/length interaction.”

Lipton in Chapter Three:

Once I understood how IMPs [Integral Membrane Proteins] worked, I had to conclude that the cell’s operations are primarily molded by its interaction with the environment, not by its genetic code.

Here Lipton is claiming that geneticists — read “genetic determinists” — think that DNA governs all the chemical reactions that occur within a cell. But not even the most fanatical genetic determinist has ever believed such a thing. DNA creates cells so that cells can act independently. That is kind of the whole point of life.

Yet Lipton accuses all scientists see genes as omniscient, all powerful dictators. All who believe them wind up being mere puppets of DNA, and the only possible remedy for this non-existent situation is to assert that environmental effects overrule the effects of genes. He talks as if any role at all played by non-genetic factors is a devastating blow to the supposed “genetic determinism” of modern science, even when the effects he cites in his laborious “Biology 101” cut-and-paste sections of the book are the routine conclusions of textbook biology.

Moreover, when geneticists relate a specific gene — deterministically — to the production of a specific protein, they are not engaging in genetic determinism. Rather, they are clearly defining limits for determinstic “genetic” influence. Once a gene has led to the manufacture of a specific protein, that protein is on its own.

This also avoids the misunderstanding that genes are intrinsically “for” some complicated illness or highly complex behavior.

And surely it is not that hard to comprehend that building a particular kind of body, with wings or fins or hands, has an effect on behavior. And that different versions of such genes (alleles) lead to variable tendencies in behavior. In the case of humans, having a hand that is capable of making a fist, and glands that are capable of producing adrenalin, clearly means that genes affect behavior. But genes also produce a big brain that is capable of learning, meaning genes also free us from being “puppets of our genes”.

And of course, variations in the way adrenalin is processed at the level of the cell can lead to variation in behavior. One version of a receptor for adrenalin in one type of brain cell may allow more adrenalin to enter a cell than other versions of that receptor. Thus more adrenalin flows through the central nervous system of one organism than happens for its compatriots. Thus a single gene that builds that cell receptor can influence behavior. But how that will play out depends on a multitude of variables at every level above that single gene.

Here we hit a fairly obvious (though easily overlooked, even by researchers) next level of influence. One might be tempted to assume that increased adrenalin levels will lead to increased aggressive behavior. But that would depend on a multitude of variables external to the adrenal system. To start from the most external: the way the person’s particular culture deals with aggression in general will affect a person’s behavior. If they are born in a culture which (at the time) values disciplined athleticism, a hot-head might find themselves getting beaten up so often that they become passive and withdrawn; in a more passive culture, they might become a tyrant. The person’s physical characteristics — a strong or weak body, for example — will obviously have a profound effect too; as will their propensity for learning and self control. The other characteristics and tendencies of the person’s nervous system; their early childhood experiences; even their experiences while still in the womb will all affect development and behavior.

And this des not even begin to consider the multitude of environmental triggers that switch genes on and off, and which Lipton seems to think scientists instantly forget about once they have discovered them.

There is nothing mysterious about this. It is all good old clunky, materialist, reductionist science, and it explains why no credible scientist today would say that “genes are fate” or that we are “puppets of our genes”, as Lipton claims mainstream scientists do. A case could be made that a particular scientist has over-emphasized the role of genes in a specific instance, (James Watson has been credibly accused of this — accused by other other geneticists), but such debate occurs well within the bounds of mainstream science. If Lipton’s teachings were the only thing standing between us and genetic determinsim, we would really be in a pickle.

Just how extreme Lipton’s environmental determinism is will become clearer in subsequent posts….. but not the next one, because that will deal with another foundational error that needs to be dealt with separately. (It concerns Lipton conflating life itself with consciousness, and thereby missing one of the most important, and perhaps genuinely spiritual, questions about the nature of human existence.)

Advertisements
h1

Bruce Lipton’s ‘Biology of Belief’ – Annotated with facts: Part 16 (Lipton’s own logic demolishes his claim that cells have a brain)

November 9, 2017

This will be a short post, because it deals with a claim that can be cleared up very easily.

In the previous post, we saw Lipton claiming to have discovered that the membrane, and not the nucleus of a cell, is the cell’s brain. He “proves” this by doing an experiment: removing a membrane and watching the cell die instantly, as a human would if you removed the brain — therefore the membrane is the “mem-Brain” of the cell.

Lipton is very excited about this, and is about to draw a great many implications from it. But there is one small problem with this logic…

We continue directly from the flaming screed of the previous post, with a new subtitle:

How the Brain Works
Once I understood how IMPs worked, I had to conclude that the cell’s operations are primarily molded by its interaction with the environment, not by its genetic code.

We don’t need to refer back to the previous post to recall what IMPs are (integral membrane proteins), because this is obviously a silly thing to say. Genes build a cell, and determine whether it is a liver cell (which carries out the functions of a liver cell), or a kidney cell. The genes also determine, in large measure, how well it will do its job. But obviously the genes in a liver cell don’t determine how much alcohol it is going to have deal with.

[As] as remarkable as these DNA blueprints are, they do not “control” the operations of the cell.

What does this mean? Does he mean that the car manufacturer doesn’t determine where the driver is going to drive to? (He implies that geneticists believe he genes do control all chemical reactions in a cell.

Logically, genes cannot preprogram a cell or organism’s life, because cell survival depends on the ability to dynamically adjust to an ever-changing environment.

Factual error. That is only one of the things a cell’s survival depends on, but it is not the only thing. And genes do indeed preprogram what kind of cell a cell is going to be.

The membrane’s function of interacting “intelligently” with the environment to produce behavior….

Lipton’s sandwich metaphor last time showed a blind chemical process by which some things get through the membrane, while others are excluded. By this measure the turnstile at the swimming pool exhibits intelligent behavior when it stops or admits people.

….makes it the true brain of the cell.

Let’s put the membrane to the same “brain” test to which we put the nucleus. When you destroy its membrane, the cell dies just as you would if your brain were removed.

Factual error.

Cells don’t necessarily die if you remove the membrane. This was cleared up some years ago by commenter @Andy, who kindly discovered and linked to this article in his comment on an earlier Lipton post:

A new technique allows scientists to study cell division without a cell membrane.

….Like a child sucking an egg out of its shell, Ivo Telley from the European Molecular Biology Laboratory… removed these cellular ‘innards’ from a fruit fly embryo, at a stage when it is essentially a sac full of membrane-less ‘cells’ that divide and divide without building physical barriers to separate themselves from each other.—-

And here is a nice movie of a “mem-Brain”-less cell still clearly alive and functioning.

Using precisely Lipton’s own logic and methodology, we can conclude that the membrane is very definitely not the brain of the cell.

Let’s make this completely clear: Lipton fabricated a scientific claim, that he attributed to mainstream science. He set out to debunk this “claim”, having himself picked the territory to demonstrate his intellectual prowess against an imaginary enemy entirely of his own creation, and winds up getting punked himself.

Dr Bruce Lipton, thanks for playing. Every conclusion he bases on his now debunked “discovery” can be dismissed out of hand.

h1

Bruce Lipton’s ‘Biology of Belief’ – Annotated with facts: Part 15 (Lipton starts lying)

November 6, 2017

Welcome to the next installment of Liptonized wallpaper that my blog has become lately. I was going to spend some more time on Chapter 2, which concludes, after leaping from mice to breast cancer, by leaping back to evolution again — groan — and to Lamarck — groan — but we have covered his errors there so many times already, that we can simply stop Chapter 2 right here — sigh of relief.

Unfortunately, it will be followed by Chapter 3.

I am going to shift gears here. I will post large tracts of Lipton’s prose, in light gray text, with little comment, and highlight in bold red text, one small part in the middle of it. I want to give a taste of how Lipton brow-beats his audience with technical Biology 101 teaching material, and then suddenly inserts a complete and utter lie right in the middle of it, and calls it “scientific”.

That lie is soon going to do a lot of heavy lifting for Lipton, and his readers will not have realized what they swallowed.

Read the rest of this entry ?

h1

Bruce Lipton’s ‘Biology of Belief’ – Annotated with facts: Part 14 (Dr Lipton plays down dangers of breast cancer, using mice)

November 5, 2017

We still haven’t made it through Chapter 2 yet, and Lipton is about to leap directly into yet another obscure and highly complex controversy in the extremely difficult subject of epigenetics. I am trying to keep all this as brief as I can, but he keeps lurching into new and often entirely unrelated topics, and there really is no choice but to tag along behind him. It’s impossible to summarize.

After overwhelming his readers with the complicated details (covered in the previous two posts), Lipton finally decides to explain to his readers what epigenetics is. He likens it to the fine tuning dials on an old-style TV set. The genes provide the actual picture, and the various dials adjust the brightness, contrast, etc.

The analogy seems passable enough, but he says little more, leaving this basic information oddly vague. Lipton fails to give his readers a coherent picture — veering between the superficial (here) and the extremely technical (previously). But at least the analogy captures the relative scales of influence. Genetics provides the basic plan (the picture), and epigenetics (fine tuning) having a much smaller, yet still potentially dramatic influence.

Lipton’s next subtitle, summing up his view of the implications of the analogy, gives our first quote for today:

Parental Life Experiences Shape Their Children’s Genetic Character

And our first commentary: Factual error.

They don’t. Not their genetic character, nor even their epigenetic character, nor their physiology. If you’re a smoker, your children won’t inherit your damaged (somatic) DNA, nor any other physical damage youu did to yourself.

We now know that the environmentally influenced fine-tuning described above can be passed from generation to generation.

As noted in the previous post, it can be passed on, in the same way that you can win lotto while skateboarding on the moon. Not only is it rare, but you also have to be on the moon and riding a skateboard in the first place. Only very specific versions of a miniscule number of genes are susceptible to passing on epigenetic traits, under very special conditions. In other words, and Lipton won’t like this, whether or not such epigenetic transference is possible, is dependent on the genes. Furthermore, the effect disappears after one or two generations.

Lipton cites one of the first such cases discovered: a study on mice by Waterland and Jirtle. (As it happens, this article is online — here it is.)

It involves a particular type of mouse — the “Agouti”. The offspring of these mice can grow up to be physiologically different, if the mother is fed a particular type of food during pregnancy. There have since been other cases of this kind of transference of epigenetic marks to offspring in other species, and it is kinda interesting if you’re into that sort of thing.

However, it does not alter DNA, so it does not contradict or even ruffle the feathers of the Central Dogma; and the effect disappears after a generation or two and so cannot affect evolution. (Just sayin’.)

Maybe I should place a chunk of prose from ‘Technical Lipton’ here, to show how he suddenly confronts his readers with terms like “maternal methyl donor supplementation”, without warning or explanation.

A landmark Duke University study published in the August 1, 2003 issue of Molecular and Cellular Biology found that an enriched environment can even override genetic mutations in mice. [Waterland and Jirtle 2003] In the study, scientists looked at the effect of dietary supplements on pregnant mice with the abnormal “agouti” gene. Agouti mice have yellow coats and are extremely obese, which predisposes them to cardiovascular disease, diabetes and cancer. Maternal methyl donor supplementation shifts coat color of the offspring from yellow to brown, and reduces the incidence of obesity, diabetes and cancer.

In the experiment, one group of yellow, obese, agouti mothers received methyl-group-rich supplements available in health food stores: folic acid, vitamin B12, betaine and choline. Methyl-rich supplements were chosen because a number of studies have shown that the methyl chemical group is involved with epigenetic modifications. When methyl groups attach to a gene’s DNA, it changes the binding characteristics of regulatory chromosomal proteins. If the proteins bind too tightly to the gene, the protein sleeve cannot be removed and the gene cannot be read. Methylating DNA can silence or modify gene activity.

This seems to be a passable enough explanation, but it is way over the heads of his readers, and a surprising contrast to his earlier simplistic TV analogy. Ultimately it only helps his readers accept his authority and assume that the things they can understand are also correct — which they, almost unfailingly, are not.

His readers will also not have noticed that this single case does not show that Parental Life Experiences Shape Their Children’s Genetic Character as Lipton claims. It only relates to a single gene in a single subspecies of mouse, under specific lab-controlled conditions. This is the kind of “mistake” that Lipton makes all the time. You don’t need a biology degree to spot it.

And for all his ranting and raving about genetic determinists, Lipton is making exactly the same mistake that the most fanatical of them were guilty of — extrapolating from lab mice directly to human beings. Only he is doing it even more fanatically than they were. This is just one case of one gene on one mouse being projected onto the whole of humanity!

And here it is, right on cue: the next sentence from Lipton suddenly starts talking about humans, as if it was a natural progression from an unusual mouse, and not a jarring change of topic.

Other studies have found epigenetic mechanisms to be a factor in a variety of diseases, including cancer, cardiovascular disease and diabetes.

Factual error. This does not belong under the heading about parental experiences affecting offspring. It is a completely different subject. Do his readers realize this?

And as noted last time in the NYT article by Carl Zimmer, epigenetic marks associated with such diseases have subsequently been shown to be a result and not a cause. From that article:

Some studies, for example, have found that people with a high body mass index have unusual epigenetic marks on a gene called HIF3A. Some researchers have suggested that those marks change how HIF3A functions, perhaps reprogramming fat cells to store more fat.
If that were true, then drugs that reverse these changes might be able to help obese people lose weight. But Dr. Smith and his colleagues have found that overweight subjects experienced epigenetic changes to HIF3A only after they put on weight….
Such claims have in fact been poorly tested, and overhyped. The study, argues that… no published results on the links between epigenetic marks and disease “can be said to be fully interpretable.”

Lipton now lurches seamlessly into his next enormously complicated topic: breast cancer.

In fact, only 5% of cancer and cardiovascular patients can attribute their disease to heredity. [Willett 2002] While the media made a big hoopla over the discovery of the BRCA1 and BRCA2 breast cancer genes, they failed to emphasize that ninety-five percent of breast cancers are not due to inherited genes.

Lipton’s wording is vague and he has garbled this in a potentially deadly fashion for his unsuspecting readers. Lipton is not an oncologist and has no business even attempting to pass out this kind of information. And he is not good with statistics, so let’s try to put that more clearly.

The BRCA1 and BRCA2 mutations are rare in that they cause about “5 percent to 10 percent of breast cancers and 10 percent to 15 percent of ovarian cancers among white women in the United States.”

But: Women who carry BRCA mutations have, on average, about a 65 percent risk of eventually developing breast cancer, as opposed to a risk of about 12 percent for most women.”

Lipton’s claim that “only 5% of cancer and cardiovascular patients can attribute their disease to heredity” seems to me to be unwarranted and misleading. The study he cites takes an entirely different perspective, noting that particular genes can predispose people to certain types of illness. The abstract is online (emphasis added):

“Genetic and environmental factors, including diet and life-style, both contribute to cardiovascular disease, cancers, and other major causes of mortality, but various lines of evidence indicate that environmental factors are most important. Overly enthusiastic expectations regarding the benefits of genetic research for disease prevention have the potential to distort research priorities and spending for health. However, integration of new genetic information into epidemiologic studies can help clarify causal relations between both life-style and genetic factors and risks of disease. Thus, a balanced approach should provide the best data to make informed choices about the most effective means to prevent disease.”

Lipton seems to be using this to score points for the ideological tick he has with genetics, and rather than concern for health of his readers. There is plenty more of this on the way too.

Worse, he makes it sound like having genes or mutations that place you at risk only increases the dangers by 5%. Lipton gives his readers the impression that because some mice exhibit an unusual reaction to parental nutrition, you can cure cancer and other illnesses with epigenetics. He might also be saying you can do this in advance for your children too, but he may not be saying that. He might have just gotten overexcited and not realized he is mixing up his errors about physiological development with his errors about evolution — which he is about to leap into as well with his very next sentence. But it is probably best to stop here for now.

h1

Bruce Lipton’s ‘Biology of Belief’ – Annotated with facts: Part 13 (Confusion about epigenetics)

October 28, 2017

I’m in the middle of moving to a new city at the moment, and I’m dependent on wi-fi and my netbook thing, so the next few posts might be a bit more widely spaced. Anyway, this is the 13th post of corrections to Bruce Lipton’s bestselling book. Not counting quotations from him, I have written (and readers have suffered through) about 18,000 words worth of corrections, and noted 68 clear factual errors. We still haven’t made it through chapter 2 yet and Lipton himself has only written 18,000 words so far!

Lipton, having decided that the nucleus of a cell is the cell’s gonads (he means this quite literally, and not merely as an atrociously inaccurate analogy), suddenly drops that topic and turns to another enormous and extremely complex field, epigenetics.

We need a little objective information about it before dealing with what Lipton tells us about it. We can use an article by scientist and science writer, Carl Zimmer, to get some perspective on this.

Epigenetics is about ‘tiny molecular caps’ that are attached at various places to DNA.

These so-called epigenetic marks are crucial to the workings of the genome: They can silence some genes and activate others. Epigenetic marks are crucial for our development. Among other functions, they direct a single egg to produce the many cell types, including blood and brain cells, in our bodies.”

As often happens with new discoveries, there is a tendency or a temptation to see their influence everywhere and overestimate their significance. The study that Zimmer reviews suggests that this has also happened in the field of epigenetics. Correlation between diseases and the presence of certain epigenetic markers raised hopes that these diseases might be treatable by removing the markers.

One of the main problems that epigenetics researchers failed to account for is the possibility that “changes to epigenetic marks don’t cause disease,” as researchers had assumed, “but are merely consequences of disease “.

Some studies, for example, have found that people with a high body mass index have unusual epigenetic marks on a gene called HIF3A. Some researchers have suggested that those marks change how HIF3A functions, perhaps reprogramming fat cells to store more fat.
If that were true, then drugs that reverse these changes might be able to help obese people lose weight. But Dr. Smith and his colleagues have found that overweight subjects experienced epigenetic changes to HIF3A only after they put on weight.”

Given that Lipton repeatedly accuses scientists of having been so obsessed with DNA that they ignored (rather than not yet discovered) epigenetic phenomena, I will note this sentence from Zimmer.

“Dr. Greally said these possibilities have been neglected because scientists have been so captivated by the idea that epigenetic marks can reprogram cells.”

This is of course more than a decade after Lipton’s book was published, so we could cut him a little slack if he has also gotten caught up in the hype. But this is where qualifiers can save a scientist from looking stupid. Time is more forgiving of those who said “it may be” or “it appears that”, than those who are now shown to have been barking up the wrong tree. (Or in Lipton’s case, something that isn’t even a tree at all, at a squirrel that never existed.)

And so, onto the next subheading in Chapter 2, Epigenetics: The New Science of Self-Empowerment

Genes-as-destiny theorists….

Factual error.

No scientist is in this category. And “destiny” is a completely vague term that does not belong to science. And recall from last time that by Lipton’s definition, “Genes-as-destiny theorists”, refers to all those scientists who believe that the ‘nucleus is the brain of the cell’…. And these scientists believe in genetic determinism…. which Lipton wrongly thinks is the Central Dogma of genetics… Which means he is referring to those biologists who accept the Central Dogma…. Which is all of them. Lipton thinks he is referring to all biologists.

…have obviously ignored hundred-year-old science about enucleated cells…

Factual error. Saying “obviously” is no substitute for evidence, of which Lipton offers none. Because there is none. Enucleation is such a routine part of biology, that it has its own special term, and wikipedia page. It is, therefore, obviously not ignored.

…. but they cannot ignore new research that undermines their belief in genetic determinism.

Factual error.

As noted repeatedly here, Lipton does not understand what genetic determinism is. It has to do with behavior, not with the genetics of physiological development.

While the Human Genome Project was making headlines, a group of scientists were inaugurating a new, revolutionary field in biology called epigenetics.

Epigenetics was not ignored, but rather, spectacularly over-hyped.

In the last decade, epigenetic research has established that DNA blueprints passed down through genes are not set in concrete at birth.

Factual error #1

“DNA blueprints” are genes. They are not “passed down through genes”.

Factual error #2

Genes are indeed set in stone (except for mutations) and are indeed passed down to subsequent generations.

Genes are not destiny!

Again, no scientist claims they are, partly because “destiny” is not a scientific concept.

Environmental influences, including nutrition, stress and emotions, can modify those genes, without changing their basic blueprint.

Correct!!!! But this contradicts what Lipton said in the previous sentence about genes not being set in stone. For the duration of this sentence at least, Lipton suddenly agrees with the Central Dogma.

And those modifications, epigeneticists have discovered, can be passed on to future generations….

Yep, in extremely rare cases, and the effects disappear after a generation or two, as they don’t alter the DNA.

… passed on to future generations as surely as DNA blueprints are passed on via the Double Helix. [Reik and Walter 2001; Surani 2001]

Factual error.

Enormous, stunningly stupid factual error. They are not passed on “as surely”. I think there have been about 30 species discovered so far where a specific one of these tiny modifications may, under specific conditions, get passed on for a generation or two. Compare that in scale to everything that DNA has passed on over the last 3 billion years or so, and that is the magnitude of Lipton’s error with that outrageous statement.

Lipton inserts some technical notes, stating that researchers in the 1950s discarded the regulatory proteins that surround the DNA. It is here that epigenetic changes occur, and Lipton describes discarding it as “throwing the baby out with the bath water. He doesn’t seem to realize that researchers needed to discover the structure of DNA before they could have discovered the epigenetic changes to it.

And then he repeats his previous monumental howler:

….and those proteins are turning out to play as crucial a role in heredity as DNA.

“As crucial a role?” I can’t believe he is claiming that. This is like saying a book mark is as important as the book.

In the 1960s, Howard Temin challenged the Central Dogma with experiments that revealed RNA could go against the predicted flow of information and rewrite the DNA.

Indeed Temin overturned Watson’s (wrong) version of the Central Dogma, but effectively confirmed the (right) version that Crick had proposed in 1958.

Originally ridiculed for his “heresy”, Temin later won a Nobel Prize for describing reverse transcriptase, the molecular mechanism by which RNA can rewrite the genetic code.

This is close enough to pass as a fairly reasonable account of what happened!!! (I always note it when I doubt Lipton but find he was right.) But….. Lipton claims that Temin’s work has been ignored. Winning a Nobel Prize is not a sign of that.

Lipton continues in this manner, as if this exception to Watson’s version of the Central Dogma means that the “primacy of the environment over DNA” has been established. Nope. It just means a previously unknown mechanism exists. The invention of the hot air balloon did not overturn the law of gravity.

It is now clear that the Primacy of DNA chart described earlier is outmoded.

Factual error #1: As shown previously, Lipton is the only person who refers to the “Primacy of DNA”.

Factual error #2: He used Crick’s triangle shaped chart to claim it’s a hierarchy which Crick did not mean — it explicitly charts flow of information. And then he switched back to using Watson’s wrong linear chart.

Factual error #3: Crick’s chart is not outmoded.

The revised scheme of information flow should now be called the “Primacy of the Environment.”

Factual error. The “revised scheme” is Crick’s 1958 model, and it already has a name — the Central Dogma.

The new, more sophisticated flow of information in biology starts with an environmental signal, then goes to a regulatory protein and only then goes to DNA, RNA, and the end result, a protein.

DNA remains unaltered by the environment and still determines which protein is made. All Lipton has done is noted the extra layers of chemical reaction that geneticists themselves have discovered. It does not contradict the Central Dogma. This is like saying the chart of a car’s brakes system needs to be overhauled and replaced with a chart of the electrical circuits.

The science of epigenetics has also made it clear that there are two mechanisms by which organisms pass on hereditary information.

Factual error.

There is certainly a multitude of epigenetic changes in a single organism’s body. But these occur only in somatic cells, not in germline cells that might get passed on — the distinction that Lipton has so far refused to tell his readers about. As noted, only a few dozen cases where certain species pass on information epigenetically is infinitesimal. Lipton should know this, and should have told his readers. Recall from an earlier post, Lipton took the time to mention August Weismann, an obscure eighteenth century biologist known only to historians of science, but somehow avoided mentioning the Weismann barrier — the crucial discovery of the difference between somatic cells (not heritable) and sex cells (that are heritable). He continues to obscure this difference from his readers and rests his entire argument here on this obfuscation.

Those two mechanisms provide a way for scientists to study both the contribution of nature (genes) and the contribution of nurture (epigenetic mechanisms) in human behavior.

Factual error.

Incredibly stupid from Lipton. Epigenetic mechanisms are not “nurture”. You do not raise your children epigenetically.

If you only focus on the blue-prints, as scientists have been doing for decades, the influence of the environment is impossible to fathom. [Dennis 2003; Chakravarti and Little 2003]

This misrepresents, misstates, and vastly oversimplifies what at least one of the cited articles actually says. Chakravarti article is available on-line, and I invite readers to read it for themselves and decide what kind of a job Lipton has done of representing this extremely complex field. I will, however, quote one sentence from it:

The inability of geneticists to easily identify common disease genes has been seen as a vindication of the importance of nurture. This is too simplistic….

 

h1

Bruce Lipton’s ‘Biology of Belief’ – Annotated with facts: Part 12 (No, cells don’t have brains or gonads, Dr Lipton)

October 18, 2017

Before we start today’s descent into Bruce Lipton’s bestseller, let me congratulate Dr Lipton on his recent induction into the prestigious Encyclopedia of American Loons. Lipton is entry No. 1899.

Bruce Lipton: now a certified American Loon

We are still wading through Chapter 2, It’s the Environment, Stupid! (“Stupid” is Lipton’s word for his biologist colleagues.)

Last time, I avoided Lipton’s pointless argument about whether or not humans have enough genes to account for our complexity. But Lipton persists, so I guess we have to look at it. The Human Genome Project turned up fewer genes than some scientists, but not others, were expecting, and Lipton sees this as a devastating blow for genetics.

We find ‘Technical Lipton’ (the version of Lipton that copies and pastes his biology lecture notes and cites highly technical papers that readers have no access to), explaining highly complex details about genetics. He assumes his readers will know what a Caenorhabditis elegans is (though he does helpfully explain that it’s a nematode worm), and assures them that Blaxter, 2003, and Celinker, et al, 2002 have done their gene counting properly.

Lipton is very excited about all this, and writes at some length, but we can cut him short. As biologist Larry Moran points out, “as we learned more and more about how genes control development, it became clear that huge differences in morphology and complexity could be due to very small changes in either the number of regulatory genes or when they were expressed. Most of the people who assimilated the advances in developmental biology began to appreciate that mammals do not need many more genes than fruit flies…”

In other words, humans having fewer genes than some scientists initially expected does not reveal any great flaw in genetics. (Note also that Moran refers to “how genes control development”, rather than Lipton’s vague talk of genes controlling “life” or “biology” or “destiny”.)

But Lipton continues obsessing about the matter, and suddenly inserts a new subheading into the middle of this discussion: Cell Biology 101.

In retrospect, scientists should have known that genes couldn’t provide the control of our lives.

This is a non-issue. Scientists don’t think that genes “control our lives”. And in fact there were some good early estimates of gene count. Moran (see previous link) quotes a 1972 estimate of about 30,000 genes for humans.

And just to get this clear, Lipton is about to attempt to solve the “problem” of how humans can be so complex with comparatively few genes — even though this is not a problem at all.

By definition, the brain is the organ responsible for controlling and coordinating the physiology and behavior of an organism.

Factual error.

What on earth is Lipton talking about? The brain does, for example, play a role in digestion of course, but it doesn’t “control” it. Nor does it “control” growth of hair or toe nails. And why does he suddenly insist that the brain does all this?

But is the nucleus truly the cell’s brain?

We need to stop right here.

The sentences I have just quoted are all sequential in the text. I haven’t cut anything out. Nor has this bizarre notion been an earlier theme which I didn’t mention. This is the first time this idea has appeared in the book.

In fact, I bet it’s the first time the idea has appeared in any book by anyone ever.

NO SCIENTIST HAS EVER SAID THE NUCLEUS IS THE CELL’S BRAIN.

What in God’s name is Lipton talking about?

If our assumption that the nucleus and its DNA-containing material is the “brain” of the cell……

No.

Just no. No. No. No. No.

Whose assumption is this? No scientist has ever ever ever ever proposed such a silly idea. No one. No time. Anywhere. Ever. No.

This is incredibly stupid. No one assumes this.

……then removing the cell’s nucleus, a procedure called enucleation, should result in the immediate death of the cell.

And if we don’t assume it is the brain of the cell — which no one does — then enucleation will just do whatever it does.

And even if we did assume that the nucleus is the brain of the cell, we would just be using a poor and utterly pointless analogy that breaks down almost immediately. What are the similarities between a brain and a nucleus? Both are enclosed in some kind of casing. Anything else?

Lipton then describes the enucleation of a cell in an absurdly theatrical manner. He is really excited about this.

But wait! It’s still moving! My God… the cell is still alive!

Who ever said it shouldn’t be?

Viable enucleated cells do not lie about like brain-dead lumps of cytoplasm on life-support systems.

And who ever said they would? Red blood cells function perfectly well without ever having had a brain.

Our experiment was designed to test the idea that the nucleus is the “brain” of the cell.

But no one ever had this stupid idea before Lipton did. No one, except Lipton, has ever suggested the nucleus is as essential to the life of a cell as the brain is to a human being. They are not even analogous. A cell has one nucleus, while the human brain has about 87 billion brain cells. That is a lot of orders of magnitude difference there.

Lipton continues, saying that this is indeed a routine experiment, and give s the history of it. So why should it be so baffling and demoralizing to scientists? What is he doing?

Then he poses another ridiculous question:

If the nucleus and its genes are not the cell’s brain, then what exactly is DNA’s contribution to cellular life?

Um, let me rephrase that for you, Dr Bruce, so that it’s not completely and utterly stupid and pointless. “What is DNA’s contribution to cellular life?”

Enucleated cells die, not because they have lost their brain but because they have lost their reproductive capabilities.

Factual error.

This is disgraceful coming someone with a PhD in cell biology. This is grade 8 biology. It’s called cell division – mitosis. Cells don’t reproduce. They replicate.

…So the nucleus is not the brain of the cell — the nucleus is the cell’s gonad!

Factual error.

Lipton should have recalled that gonads produce cells that have half a set of chromosomes. Sexual reproduction is not like cell division. Okay, they both have similar names — mitosis and meiosis, but why say that one is the other? Even as an analogy this is way off target. Even the brain would be a better analogy for a cell nucleus. But I don’t think Lipton means it as a mere analogy. I think he sees a real equivalence of functions beyond this single distant not-quite-parallel.

Confusing the gonad with the brain is an understandable error because science has always been and still is a patriarchal endeavor.

Factual error. As noted, no scientist, not even the most patriarchal has ever suggested the nucleus is the brain of the cell.

Males have often been accused of thinking with their gonads, so it’s not entirely surprising that science has inadvertently confused the nucleus with the cell’s brain!

Lipton keeps yukking it up over this, and his readers are unaware that there is only one scientist who has ever had this stupid idea that the nucleus is the brain of the cell. And only one scientist has ever taken the time to disprove it. And only one scientist has ever decided that the nucleus is the gonad of the cell — an idea even more stupid than the idea of the brain being that.

This is, I think, the stupidest thing Lipton has written in this book yet. But there is still plenty more to come just in chapter 2.

h1

Bruce Lipton’s ‘Biology of Belief’ – Annotated with facts: Part 11 (Two distinct styles & punked by Darwin again)

October 16, 2017

And now back to this marathon of wading through Lipton’s bestseller. We are still in Chapter 2, It’s the Environment, Stupid!

I will start quoting a few of Lipton’s more technical passages. I’ve been leaving these out so far and only indicating their contents, as they are often uncontroversial and sometimes irrelevant or too detailed for a popular work. But it is perhaps worth quoting them sometimes though, just to show how striking the contrast is between ‘Technical Lipton’, who explains normal biology in normal terms, and ‘Lipton the Destroyer’ who has it in for the whole of genetics and biology.

I am certain that ‘Technical Lipton’ simply copies and pastes passages from his old biology essays from university. He often opens such passages with a snide but nevertheless vague attack on modern genetics or Charles Darwin, then pastes part of an old essay, (which frequently in fact support the very ideas he is trying to attack); and then ends the paragraph with a sudden switch back to vague but livid invective from ‘Lipton the Destroyer’ for a closing sentence.

Maybe I am being unfair by guessing he’s copying and pasting old essay content, but two very distinct styles are plainly visible.

‘Technical Lipton’ explains the discovery of the structure of DNA.

In 1910, intensive microscopic analyses revealed that the hereditary information passed on generation after generation was contained in chromosomes, thread-like structures that become visible in the cell just before it divides into two “daughter” cells. Chromosomes are incorporated into the daughter cell’s largest organelle, the nucleus. When scientists isolated the nucleus, they dissected the chromosomes and found that the hereditary elements were essentially comprised of only two kinds of molecules, protein and DNA. Somehow the protein machinery of life was entangled in the structure and function of these chromosome molecules.

The understanding of the chromosome’s functions was further refined in 1944 when scientists determined that it was DNA that actually contained hereditary information. [Avery, et al, 1944; Lederberg 1994] The experiments that singled out DNA were elegant. These scientists isolated pure DNA from one species of bacteria— let’s call it Species A— and added the pure DNA to cultures containing only Species B bacteria. Within a short time. Species B bacteria began to show hereditary traits that were formerly seen only in Species A….

That seems fairly straight forward to me. Well structured, and clearly explained. The style is remarkably different from both the vocabulary and syntactical structure that ‘Lipton the Destroyer’ uses when he suddenly starts attacking Darwin and hectoring his former colleagues.

The way he cites sources as if for an academic paper makes me think he is simply pasting in stuff from his old essays. Obviously, in a science book for a popular audience there is no reason to interrupt the text with citations to support a noncontroversial historical event that is quite irrelevant to his topic. I’ve never seen any science writer, even in specialized books, cite things in this way before. But it is the standard referencing style for university essays.

And in this case, like every other case in this book it’s pointless. No one doubts that Avery did this in 1944, nor do they care that Lederberg wrote a paper to honor them 50 years later, but there it all is, cited in the text and referenced in the bibliography:

Avery, O. T., C. M. MacLeod, et al. (1944). “Studies on the chemical nature of the substance inducing transformation of pneumococcal types. Induction of transformation by a deoxyribonucleic acid fraction isolated from Pneumococcus Type III.” journal of Experimental Medicine 79: 137158

Lederberg, J. (1994) Honoring Avery, MacLeod, And McCarty: The Team That Transformed Genetics. The Scientist 8: 11.

This is why Lipton’s fans have left comments on other posts here insisting that his claims are well supported in his book. They haven’t realized that the only thing Lipton has bravely supported here is the fact that Avery did groundbreaking work in genetics in 1944.

And then, the very next sentence from Lipton is this:

….Once it was known that you needed nothing other than DNA to pass on traits, the DNA molecule became a scientific superstar.

And with that, ‘Technical Lipton’ is again replaced with ‘Lipton the Destroyer’. The entire book alternates between these two modalities. No substantive effort is made to connect the hyperbole to the sensible content, beyond blank assertions that geneticists think that DNA is now the superstar.

He continues the snarky style for the opening sentence of the next paragraph:

It was now left to Watson and Crick to unravel the structure and function of that superstar molecule….

This is the hyperbolic intro to some more of his sensible sounding Bio 101 essays.

….DNA molecules are long and threadlike. They are made from four nitrogen-containing chemicals called bases (adenine, thymine, cytosine, and guanine or A, T, C and G). Watson and Crick’s discovery of DNA’s structure led to the fact that the sequence of the A, T, C and G bases in DNA spells out the sequence of amino acids along a protein’s backbone [Watson and Crick 1953]. Those long strings of DNA molecules can be subdivided into single genes, segments that provide the blueprint for specific proteins….

He adds a slightly hyperbolic sentence to end the paragraph:

…The code for recreating the protein machinery of the cell had been cracked!

(This refers to an earlier description of “protein as a machine”, which I didn’t include last time.) Then more Bio 101 notes.

Watson and Crick also explained why DNA is the perfect hereditary molecule. Each DNA strand is normally intertwined with a second strand of DNA, a loosely wrapped configuration known as the “double helix.” The genius of this system is that the sequences of DNA bases on both strands are mirror images of each other. When the two strands of DNA unwind, each single strand contains the information to make an exact, complementary copy of itself. So through a process of separating the strands of a double helix, DNA molecules become self-replicating…..

Note the way this praises “the genius of this system”, and is entirely free of his usual invective and sneering. Then he tacks the usual vague, inaccurate and snarky final sentence onto the end:

….This observation led to the assumption that DNA “controlled” its own replication… it was its own “boss.”

Despite the quote marks around “controlled” and “boss”, Lipton is not citing Watson & Crick, or any other geneticist. This is because the sentence is devoid of meaning. Geneticists don’t use such vague terms.

The “suggestion” that DNA controlled its own replication…

Again, no one suggested or even with nonsensical scare quotes “suggested” this. At least no one except Lipton. Note too, how Lipton presents Crick and Watson as anthropomorphizing DNA.

…and also served as the blueprint for the body’s proteins led Francis Crick to create biology’s Central Dogma, the belief that DNA rules….

This is just weird. Crick didn’t think along these lines. The idea is meaningless. Note that Lipton has not once clearly told his readers what the “Central Dogma” is, despite referring to it repeatedly and making its refutation his central issue.

We may as well note here too, that when Crick jokingly made up the term Central Dogma, he didn’t know what a dogma is. Being ignorant of church customs, he thought it meant law. Had he chosen a better label, he probably would have saved everyone a lot of pointless arguments.

The dogma is so fundamental to modem biology it is essentially written in stone, the equivalent of science’s Ten Commandments.

Factual error. The central dogma works — that’s why, despite constant challenges by hotheaded biologists who charge at it like a wounded elephant, it is still on the books.

What Lipton needs to do is show why it is wrong. And of course he doesn’t. He can’t do that if he doesn’t know what it is.

In the dogma’s scheme of how life unfolds, DNA perches loftily on top, followed by RNA.

Factual error.

Here is the original diagram from Crick’s 1958 paper.

Crick: (left) possible paths of flow of chemical “information”, and (right) actual flow

Lipton is wrong to say the diagram indicates primacy or bossiness of DNA. The first triangle shows all possible flow paths of information between three elements. The second shows the flow paths which he held (correctly) to be the actual ones. Lipton wrongly claims that Crick meant it as a power hierarchy where DNA “has primacy” or is the “boss” of all subsequent chemical reactions that supposedly occur ‘under’ the DNA.

RNA is the short-lived Xerox™ copy of the DNA. As such, it is the physical template encoding the amino acid sequence that makes up a protein’s backbone. The Primacy of DNA diagram provides the logic for the Age of Genetic Determinism.

Factual error.

As we saw this is not the “logic” of anything in genetics. Lipton has simply not understood the diagram and is making false accusations against his “stupid” colleagues.

And worse, he is insisting again on his stunningly stupid error that the central dogma is genetic determinism. As Wikipedia would have told him, genetic determinism is “the belief that human behavior is controlled by an individual’s genes”. It is not the central dogma, and only looks like it is if you don’t know what the central dogma is. Note too that wikipedia has no problem dismissing it as a “belief”, whereas Lipton implies it is central to all of biology.

Because the character of a living organism is defined by the nature of its proteins, and its proteins are encoded in the DNA, then by logic, DNA would represent the “first cause” or primary determinant of an organism’s traits.

Factual error.

This is not how science is done. There is no idea that DNA must logically have primacy over the rest of the organism in this vague manner that Lipton imagines. He is misleading his readers here.

Then Lipton suddenly veers off to talk about Copernicus and the Church, and the human genome project. We need not follow him down this rabbit hole, but we can note the point he was trying to make. The human genome project found that humans have fewer genes than some researchers expected. Some saw great significance in this, and some, including Lipton, still do. It is however insignificant and irrelevant, so we will ignore it. Anyone interested in the issue Lipton’s is excited about can read this on the topic.

After this pointless detour, it’s suddenly back to the central dogma again. And Lipton is about to finally about tell his readers exactly what the central dogma is…. And of course he gets it wrong.

The Central Dogma. The dogma, also referred to as the Primacy of DNA, defines the flow of information in biological organisms….. [T]he flow is only in one direction, from DNA to RNA and then to Protein.

Factual error.

As we saw in the diagram above, a dotted line runs from RNA back to DNA — in other words, in two directions. We covered this in Part 1, but you can read a real biologist explaining it all here.

The DNA represents the cell’s long-term memory, passed from generation to generation.

Correct!!!! Even the analogy!!!!

No new “information” flows from outside the DNA back in…. But this is exactly what the central dogma says. And despite what Lipton just wrote in the previous sentence, he now suddenly agrees with it — maybe because he is copy and pasting from an old essay.

RNA, an unstable copy of the DNA molecule, is the active memory that is used by the cell as a physical template in synthesizing proteins. Proteins are the molecular building blocks that provide for the cell’s structure and behavior.

Ok, but note the use of the word “behavior”, with its metaphorical meaning.

DNA is implicated as the “source” that controls the character of the cell’s proteins…

Factual error.

DNA is not the “source” of proteins. It determines which proteins are manufactured, out of chemicals in the cell.

This is not science. And all these words, source, controls, character, behavior, are too slippery to describe processes that are well understood. We already know that Lipton wants to anthropomorphize all this. He can if he wants to argue for it, but he can’t do it and call it the Central Dogma of genetics.

…hence the concept of DNA’s primacy that literally means “first cause.”

Factual error.

There is no “concept of DNA’s primacy” in genetics. Lipton has invented this and ascribed it to the science of genetics. Is he deliberately lying to his readers? The only hits google turns up are for either Lipton or people quoting him.

Lipton is giving his readers false information about science and then “correcting” it with even more false information.

Then Lipton suddenly veers back again to the Human Genome Project finding fewer genes than expected. It’s not an issue (see earlier link), but Lipton insists that this is inexplicable for science.

We can no longer use genes to explain why humans are at the top of the evolutionary ladder.

Factual error.

There is no evolutionary ladder. And any idea of humans being at the top of such a thing was blown out of the water in one decisive hit by the very scientist Lipton has cited and attacked more often than any other.

That book, of course, demolished the notion of some species being superior to others, and instead defined ‘fitness’ as relative to an organism’s particular habitat. Had Lipton read and understood this book he would have spared himself a great many errors. Instead, he finds himself yet again getting punked by Charles Darwin.