1. Large Hadron Collider readies for world's biggest experiment

Comment #243161 by jeremynel on September 5, 2008 at 8:18 am

"What we find honestly depends on what's there," said Brian Cox

One would sincerely hope so.

2. Monogamy gene found in people

Comment #241397 by jeremynel on September 2, 2008 at 7:20 am

It might be appropriate here to remind people of Richard's excellent essay entitled "Genes aren't us", from A Devil's Chaplain.

3. Genesis and the origin of the Origin of the species

Comment #239570 by jeremynel on August 29, 2008 at 11:54 pm

I love how he uses the nebulous, abstract God in this article. As P.Z. Myers said of this "confusion between different concepts of this god-thingie":

Theologians play that one like a harp, though, turning it into a useful strategem. Toss the attractive, personal, loving or vengeful anthropomorphic tribal god to the hoi-polloi to keep them happy, no matter how ridiculous the idea is and how quickly it fails on casual inspection, while holding the abstract, useless, lofty god in reserve to lob at the uppity atheists when they dare to raise questions...It gets annoying. We need two names for these two concepts, I think. How about just plain "God" for the personal, loving, being that most Christians believe in, and "Oom" for the bloodless, fuzzy, impersonal abstraction of the theologians? Not that the theologians will ever go along with it�quot;the last thing they want made obvious is the fact that they're studying a completely different god from the creature most of the culture is worshipping.

With this God in tow, he can happily admit that the argument from design is awful - he has a thousand more "mysteries" with which to prop God-the-latter up.

The second half of the article alternates between vacuous and erroneous. For instance, "the curious paradox, noted by Richard Dawkins, that selfish genes get together and produce selfless people" is only superficially a paradox, and has been resolved by (amongst others) the very same author, in his very first book.

4. Scientists Create Blood From Stem Cells

Comment #234278 by jeremynel on August 21, 2008 at 4:25 am

People usually require blood transfusions that match their own blood type: A mismatch can be fatal. Type O-negative can be safely transferred into anyone, but is only possessed by about 7 percent of the population, leaving supplies perpetually short.

Well, not exactly. The two antigen systems most likely to generate an immune response are the ABO and Rhesus (i.e. postive or negative) blood groups.

However, there are hundreds of antigens on the surface of red cells, and so giving O negative blood (which lacks both the main sets of antigens, and thus is won't provoke an immune response against them) can still quite easily result in a transfusion reaction against one of the other antigens. See, for instance, here for more details.

To avoid this, a sample of the patient's blood is always crossmatched against the potential transfusion sample - after the ABO and Rhesus systems have been matched, to see whether the two will nonetheless react. The only time you blindly give O negative blood to a patient is in a dire emergency, when there isn't time for the above procedure.

HOWEVER, this is still a massive breakthrough that will eventually save countless lives. Even if there are more antigens than the ABO and Rhesus sets, having more O negative blood around will greatly increase the chances of finding compatible blood, since the odds of one of the other antigens causing a transfusion reaction are quite small anyway.

5. Religions thrived to protect against disease

Comment #222090 by jeremynel on July 30, 2008 at 2:59 pm

Even if the serious objections about methodology, correlation vs cause, etc. could be bypassed, this would STILL only favour a form of xenophobia or in-group solidarity vs out-group antagonism.

This sort of rationale (the avoidance of disease) does NOT explain believing in imaginary friends, everlasting life and fatherless men.

Rather irritating.

6. Good Science Writers: Richard Dawkins

Comment #216557 by jeremynel on July 23, 2008 at 9:37 am

I am interested in the suggestion that Climbing Mount Improbable might not be an ideal title. Interested, because I regard it as the most under-rated of my books.

Richard,

Surely the most under-rated of your books would be "The Extended Phenotype"? I've personally never read anything so brilliant, and yet it's hard to find it on bookshelves (whereas none of your other books are, including Climbing Mount Improbable).

7. New discovery proves 'selfish gene' exists

Comment #197707 by jeremynel on June 22, 2008 at 2:11 pm

This article is terrible, as many of the above commenters have pointed out. I pity the poor scientists who made the discovery (not the discovery alleged in the title, of course; that would apparently be asking too much). They have been totally misrepresented.

8. Stupid flies live longer: study

Comment #189415 by jeremynel on June 6, 2008 at 8:25 am

Thanks somersetsimon, I think you're probably right.

Steven, I didn't mean to imply that I thought they were inheriting memes - or anything similar. What I was questioning was how learning acquired by Pavlovian tests leads to increased mental capacity in the flies' descendants. It clearly doesn't, of course. Somersetsimon has nicely rectified the rather dismal reporting, I think. Apologies if I didn't phrase things well enough.

9. Stupid flies live longer: study

Comment #189356 by jeremynel on June 6, 2008 at 5:46 am

One half was left in a natural state while the other had its intelligence boosted by Pavlovian methods, such as associating smell and taste with particular food or experiences.

Over 30 to 40 generations, these methods led to flies which clearly learned better and remembered things for longer.

No doubt this is due to a deficiency in the reporting, but the above quote puts the flies' increased intelligence down to Lamarkian evolution!

Does anyone know how the one group of flies actually became more intelligent?

10. Altruism in social insects is a family affair

Comment #186279 by jeremynel on May 30, 2008 at 3:56 am

I agree - science at its best.

If it's of interest to anyone, Wilson's 2005 case against kin selection being the explanation for eusociality can be found here.

There was a reply to the challenge published by Foster et al. here

... which was in turn criticised by, amongst others, David Sloan Wilson, here.

And, finally (!) in this article, Foster et al. fend off the lastest criticism of kin selection.

Whew! I fear that the above is only really accessible for people with some background knowledge of the issues, but it if you make the effort, it makes absolutely fascinating reading.

11. What Genes Remember

Comment #184790 by jeremynel on May 26, 2008 at 7:25 am

This article was quite unclear, at least to me. In my opinion:

1. Epigenetics in general poses absolutely no challenge to evolution. Epigenetics is basically the study of environmentally-induced changes in the expression of genes. For example, kidney cells express "kidney" genes whereas liver cells express "liver" genes, despite both types of cells containing the same DNA. As the article concedes, this has been known since the 1940s, and is fully compatible with evolutionary theory.

2. Almost all the epigenetic changes are confined to somatic cells - they don't affect the germ-line cells of our ovaries or testes. Thus, to a first approximation, epigenetic changes aren't inherited, and so the gene remains utterly unchallenged as the unit of selection in evolution.

3. Where epigenetics really could induce a (minor) change to our understanding of evolution is in the subset of epigenetic changes which do seem to have the potential to be inherited. However, as the article itself states, epigenetic inheritance "can readily be reversed, and there is as yet little or no evidence that it persists for longer than a few generations." As yet, we need more data on this topic...

12. Regulating Evolution: How Gene Switches Make Life

Comment #175790 by jeremynel on May 6, 2008 at 3:28 am

Regretfully, the word "gene" is used in many different senses by various disciplines. This doesn't hinder the experts, but laymen can be misled.

The authors here use "gene" to mean that part of the DNA that is transcribed into mRNA and thus a protein. This is often how the word is used by molecular biologists.

However, the word "gene" in Williams'/Dawkins' sense refers to that part of the genetic code that acts as a unit for long enough to by effectively selected for by natural selection. It is not limited to those parts of the genome that happen to be transcribed.

Thus, while it is certainly true in the molecular biologists' sense that "[i]f humans want to understand what distinguishes animals, including ourselves, from one another, we have to look beyond genes", this would not be true if "gene" were being used in Dawkins' sense. Since the things regulating the transcription of genes are THEMSELVES heritable (they're also DNA!), stable, and have phenotypic effects, they are genes to Dawkins (and many others).

Nice article, by the way.

13. Gunk in T. Rex Fossil Confirms Dino-Bird Lineage

Comment #169162 by jeremynel on April 25, 2008 at 3:23 pm

Apologies - I've just read the other similar article posted here on this topic, and it does seem (if I've read it right) that the *actual* protein was preserved. That's astounding - I had no idea proteins (even tough ones like collagen) could last even a fraction of this length of time. Wow.

14. Gunk in T. Rex Fossil Confirms Dino-Bird Lineage

Comment #169156 by jeremynel on April 25, 2008 at 3:18 pm

Apologies in advance for the ignorance, but from the article I'm not sure whether they are referring to *actual* "soft tissue" and "proteins" still preserved after 68 million years ago, or merely their fossilised replicas.

I'd be really surprised (and enormously encouraged) if the former were true, but is it perhaps too much to ask? Can anyone here advise?

15. Biologists Take Evolution Beyond Darwin Way Beyond

Comment #156264 by jeremynel on April 7, 2008 at 7:58 am

"Selection probably happens at all scales, from gene to individual to species to collection of species to ecosystem to we don't even know what," said Maya Paczuski, head of the Complexity Science Group at the University of Calgary.

Paczuski's group sees evolution as taking place at all these levels, with what happens in ecosystems rippling down to individuals, back up to populations, across to other populations, and so on -- all simultaneously, and in tandem with the mysterious dynamics of networked complexity.

Big gadget, this is Little Tool. We've got ourselves a situation.

16. The Group Delusion

Comment #110459 by jeremynel on January 11, 2008 at 8:23 am

Richard,

I can almost feel your anguish from here. For my part, I've always found your evolutionary reasoning to be crystal-clear, even when guiding me over areas where I might otherwise have stumbled. So clear are your explanations, in fact, that I am still deeply perplexed at how someone could still be making the sorts of errors about which you've written. Reading, say, S.J. Gould or D.S. Wilson, is somewhat of a painful experience.

My sympathies, then.

17. The empty myths peddled by evangelists of unbelief

Comment #97507 by jeremynel on December 12, 2007 at 8:07 am

In his book The Selfish Gene, Dawkins argues ... humans are "gene machines" programmed by evolution to replicate themselves.

Wow, did he miss the point, or what?

Contrast with the actual phrase and spot the absolutely vital difference (the entire point of the book?):

We are survival machines - robots blindly programmed to preserve the selfish molecules known as genes."

18. I didn't know the FLEA CIRCUS was back in town!

Comment #84999 by jeremynel on November 4, 2007 at 1:15 pm

you'd think that if the apologetics had a valid response, one book would suffice

Reminds me of the time when Nazi Germany sponsored a book entitled "100 scientists against Einstein".

Einstein's response: "If I'd been wrong, 1 would have sufficed."

19. Evolution to be taught in SA schools

Comment #82852 by jeremynel on October 28, 2007 at 3:17 am

As a South African, I have very much mixed feelings about the article.

The comments by the teachers and even by the administrators are stupid, and deeply depressing.

Yet recall that Grade 12 is the final year before entering university, and that "life sciences" is basically the new name [wince] for biology. Evolution was always mentioned implicitly before, but to expand its weighting as part of the new curriculum is very encouraging, if LONG overdue.

Perhaps after a few years, even the teachers will be educated.

20. Downward, Christian soldier

Comment #80650 by jeremynel on October 22, 2007 at 1:48 pm

What is unacceptable is that he does not keep the miracle to himself, that he aspires to proselytise, inculcate, enjoin or encourage people in a disciplinary hierarchy under him to think and act in line with those personal views, that he does so in a context in which people who have volunteered to put themselves in harm's way are being treated in his remarks as moral children needing to be solaced with fairy stories, and that what he is saying - clearly without recognising the irony, the bitter irony - is a version of the rubbish that impels people of a different (and from the general's point of view - were he consistent - blasphemous and false) faith to kill and die also, too many of them as suicide bombers attacking the innocent, believing in a life after death full of rewards, and enjoying spiritual strength as they seek them through murder and mayhem.

What a long sentence.

21. The Komodo Dragon's Tale

Comment #14945 by jeremynel on December 27, 2006 at 3:51 am

Thanks for clearing things up, Prof, and for a wonderful article. FYI: if you do get to read this, The God Delusion has been one of the Top 5 best-selling books in the major bookstore chain in South Africa (www.exclusivebooks.co.za) for months now. Keep up the magnificent work - it truly does inspire others. :)

22. The Komodo Dragon's Tale

Comment #14933 by jeremynel on December 26, 2006 at 11:35 pm

"But New Scientist failed to mention a third possibility..."

Does that imply that RD is the first to (albeit theoretically) work out how the Komodo Dragon reproduced so?